/data/tool/gcphrap aa.fasta.screen -ace -view -exp /data/ultra_disk/people/tomato/t1/e0111p12/workdir/all.assembly 
gcphrap version 0.990319

Run date:time  080625:095932
Query file(s):  aa.fasta.screen
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 14, maxmatch: 30, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 80
word_raw: 0
trim_penalty: -2, trim_score: 20, trim_qual: 13, maxgap: 30
repeat_stringency: 0.950000
qual_show: 20
confirm_length: 8, confirm_trim: 1, confirm_penalty: -5, confirm_score: 30
node_seg: 8, node_space: 4
forcelevel: 0
max_subclone_size: 5000

Sequence file: aa.fasta.screen    1154 entries
Residue counts:
  A    341579
  C    200581
  G    202406
  N    11604
  T    323483
  X    60168
Total  1139821

Read name analysis:
 # Reads      # templates
   1          1154

 Suffix counts:
(no suffix) 1154


Templates inferred from description field:     0
Templates inferred from name field:         1154

Read-template multiplicity analysis:
 # Reads      # templates
   1          1154

Chemistries inferred from description field:
    0  dye-primer
    0  old-dye-terminator
    0  big-dye-terminator
    0  other

Chemistries inferred from name:
 1154  dye-primer
    0  old-dye-terminator
    0  big-dye-terminator
    0  other

Directions inferred from description field:
    0  fwd
    0  rev
    0  unknown (set to fwd)

Directions inferred from name:
    0  fwd
    0  rev
 1154  unknown (set to fwd)

Quality file: aa.fasta.screen.qual

Input quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56  127101  11.2  127101  11.2    0.32
 51   72081   6.3  199182  17.5    0.89
 50   26053   2.3  225235  19.8    1.15
 48    4374   0.4  229609  20.1    1.22
 47    3455   0.3  233064  20.4    1.29
 46   15325   1.3  248389  21.8    1.68
 45   26676   2.3  275065  24.1    2.52
 44   21092   1.9  296157  26.0    3.36
 43   45745   4.0  341902  30.0    5.65
 42   63900   5.6  405802  35.6    9.68
 41   18034   1.6  423836  37.2   11.12
 40   57887   5.1  481723  42.3   16.90
 39    5476   0.5  487199  42.7   17.59
 38    8779   0.8  495978  43.5   18.99
 37   23898   2.1  519876  45.6   23.75
 36    3718   0.3  523594  45.9   24.69
 35   34608   3.0  558202  49.0   35.63
 34    8704   0.8  566906  49.7   39.10
 33   12515   1.1  579421  50.8   45.37
 32   13208   1.2  592629  52.0   53.70
 31    5363   0.5  597992  52.5   57.96
 30    6538   0.6  604530  53.0   64.50
 29   23617   2.1  628147  55.1   94.23
 28    6743   0.6  634890  55.7  104.92
 27   11240   1.0  646130  56.7  127.35
 26    5245   0.5  651375  57.1  140.52
 25   13689   1.2  665064  58.3  183.81
 24   11918   1.0  676982  59.4  231.26
 23    9088   0.8  686070  60.2  276.80
 22    8998   0.8  695068  61.0  333.58
 21   10783   0.9  705851  61.9  419.23
 20   10193   0.9  716044  62.8  521.16
 19   16442   1.4  732486  64.3  728.15
 18    9931   0.9  742417  65.1  885.55
 17   11287   1.0  753704  66.1  1110.75
 16   13964   1.2  767668  67.3  1461.51
 15   15397   1.4  783065  68.7  1948.41
 14   13607   1.2  796672  69.9  2490.11
 13   22175   1.9  818847  71.8  3601.50
 12   18885   1.7  837732  73.5  4793.06
 11   28802   2.5  866534  76.0  7080.88
 10   39586   3.5  906120  79.5  11039.48
  9   69228   6.1  975348  85.6  19754.77
  8   52832   4.6  1028180  90.2  28128.08
  7   32196   2.8  1060376  93.0  34552.03
  6   44047   3.9  1104423  96.9  45616.13
  4   23595   2.1  1128018  99.0  55009.47
  0   11216   1.0  1139234  99.9  66225.47
 -1     587   0.1  1139821 100.0  66812.47   (quality -1 = terminal quality 0)

Avg. full length: 987.7, trimmed (qual > -1): 987.2
Avg. quality: 30.0 per base

Exact duplicate reads:  None.

Probable unremoved sequencing vector (matches excluded from assembly, quality reduced to 0): 
aa020109r1   52-52   C
aa060109r1   15-54   GACTCCGCGCGGTGGCGGCCGCTCTAAACTAGTGGATCCT
aa090109f1   15-35   TGTATCGAATTCCTGCAGCCC
aa110109f1   15-36   TTGTATCGAGTTCCTGCAGCCC
aa110109r1   16-56   ACTCCTCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTCC
ab020109f1   35-35   C
ab060109r1   52-55   CCCC
ab070109f1    9-34   TAAGCTGTATCGAATTCCTGCAGCCC
ab070109r1   22-52   CGGTGGCGGCCGCTCTAGACTAGTGGATCCT
ab100109r1   12-54   TGTACTCCCGCGGTGGCGGCCGCTCTATACTAGTGGATCCCCC
ab120109r1   13-55   TGTACTCCCGCGGTGGCGGCCGCTCTACACTAGTGGATCCCCC
ac010109f1   21-41   CGAATTCCTGCAGCCCCTCGC
ac010109r1   55-59   TTTAC
ac020109f1   14-27   TCGAATCCTGACCC
ac020109r1   22-54   CGGTGGCGGCCGCTCTAGACTAGTGGATCTTCC
ac120109r1    8-55   TTGAAGGGACGCTCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCCCC
ae030109r1   16-51   CCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTTTC
ae120109r1   16-55   ACTCCCGCGGTGGCGGCCGCTCTAAACTAGTGGATCCCTC
af100109r1   53-54   CC
ag060109r1    8-55   TTGAAGGGACGCGCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTCC
ag070109r1   13-55   GGGACCCTCGCGGTGGCGGCCGCTCTANACTAGTGGATCCTCC
ag120109f1   18-19   AT
ah020109r1   17-57   ACTCCCCGCGGTGGCGGCCGCTCTANACTAGTGGATTCTTC
ba040109f1    1-29   AAAACTTTGTATTCGAATTCCTGCAGCCC
ba090109f1    4-22   TTGTATCGATTCTGCGCCC
ba090109r1   19-50   GGTGGCGGCCGCTCTAGACTAGTGGATCTTTC
bb070109f1    1-25   TAAACTGTATCGATTCCTGCGCCCT
bb070109r1   18-49   CGGTGGCGGCCGCTCTAGACTAGTGGATCCTT
bb110109f1   13-30   ATCGAATTCCTGCAGCCC
bb120109r1    9-49   ACTCCTCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTTC
bc010109f1   16-31   CGAATTCCTGCAGCCC
bc010109r1   46-50   TTTTC
bc100109f1   30-32   TTT
bd040109f1    2-29   AAAACTTTGTAATCGAATTCCTGCAGCC
bd060109r1    1-50   GATAGGTGACTCCACGCGGTGGCGGCCGCTCTANACTAGTGGATCCTTCC
bd110109f1   13-14   AT
be080109f1    6-27   TGTATCGAATCCTGCGCCCTTT
bf040109r1    9-50   GACTCCGCGCGGTGGCGGCCGCTCTANACTAGTGGATCCTTC
bf050109r1    9-50   GACTCCTCGCGGTGGCGGCCGCTCTANACTAGTGGATTCTCC
bf080109r1    9-45   GACTCCGCGCGGTGGCGGCCGCTCTAGACTAGTGGAT
bf120109r1    2-46   GATTTGGGACTCCACGCGGTGGCGGCCGCTCTAGACTAGTGGATC
bg060109r1   47-47   C
bh120109r1    2-45   GTAAGGCGACTCCCCGCGGCGGCGGCCGCTCTAGACTAGTGGAT
ca050109r1    8-45   GACTCCACGCGGTGGCGGCCGCTCTAGACTAGTGGATT
cb010109f1    4-30   ACTTGATATTCGAATTCCTGCAGCCCT
cb120109r1   36-50   ACTAGTGGATTTTTC
cf020109f1   12-27   TCGATTCCTGCAGCCC
cf020109r1   18-50   CGGTGGCGGCCGCTCTAGAATAGTGGATCCTCC
cf040109f1   30-36   CGTAGGA
cg030109r1   11-42   CCCGCGGTGGCGGCCGCTCTAAACTAGTGGTT
cg050109f1   10-27   ATCGGAATCCTGCAGCCC
db080109r1   47-47   C
db120109r1    9-50   GACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTCTCC
dc070109r1    6-48   GACTTCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCTCTTC
dc090109r1    6-44   GGGGACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGA
dc100109r1    7-50   GGGACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCTCCC
dd040109f1    5-28   CTTGTATTCGAATTCCTGCAGCCC
dd080109r1    3-47   GGGGACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTCC
de120109r1   11-45   CCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTCT
df010109r1    9-58   ACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTTTCCTCCTTCTCC
df070109r1   48-48   C
dg080109r1    1-46   TGGGGGACTCCCCGCGGTGGCGGCCGCTCTGTACTAGTGGATCCTC
ea010109f1    2-29   AAACTTTGTATTCGAATTCCTGCAGCCC
ea020109r1   13-47   CCGCGGTGGCGGCCGCTCTAGACTAGTGGATTTTC
ea050109f1   30-30   C
ea060109f1   27-31   CCCAC
ea060109r1    9-50   GACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTCC
ea100109f1   28-29   CC
ea120109f1    1-27   AAACCTGGTAATCGAATTCCTGCAGCC
eb050109r1    2-45   GTAAGGGGACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGAT
eb060109r1    9-48   GACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCT
eb070109f1    3-29   AAACTTTGTATTCGAATTCCTGCAGCC
eb080109r1    9-50   GACTCCGCGCGGTGGCGGCCGCTCTAGACTAGTGGATCTTTC
ec010109f1    1-33   AAACTTTGATATCCGAATTCCTGCAGCCCAGCA
ec050109r1    7-47   ACTCCGCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCCCC
ec120109f1    1-29   AAACCTTGTTATCCGAATTCCTGCAGCCC
ec120109r1    8-49   GACTCCTCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTCC
ed010109r1    1-49   GATTGGTGACTCCCCGCGGTGGCGGCCGCTCTANACTAGTGGATCTCCC
ed060109f1   15-27   ATTCCTGCAGCCC
ed060109r1   12-48   CCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTTC
ee050109r1   14-49   CCCGCGGTGGCGGCCGCTCTAGACTAGTGGATCCTC
ee100109f1   30-30   C
ee120109r1    6-44   GGGACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGAT
ef030109r1   14-49   CCCGCGGTGGCGGCCGCTCTANACTAGTGGATTTTT
ef070109f1    1-29   AAACCTTGGTATCCGAATTCCTGCAGCCC
ef080109r1    2-53   GATAGGGGACTCCCCGCGGTGGCGGCCGCTCTAGNAACTAGTGGNATCCTCC
eg030109r1    9-49   GACTCCCCGCGGTGGCGGCCGCTCTAGAACTAGTGGTTTTT
eg100109f1    2-32   AAACCTTGTTATCGAATTCCTGCAGCCCGGC
fa100109r1   44-60   ACTAGTGGGATTTTTCC
fa110109r1   15-49   CCGCGGTGGCGGCCGCTCTACACTAGTGGATTTTC
fc110109f1    1-28   AAACCTTGTTATCGAATTCCTGCAGCCC
fc110109r1    9-52   GACTCCACGCGGTGGCGGCCGCTCTANACTAGTGGATCTCTTCC
fd040109f1    1-29   AAACCTTGATAATCGAATTCCTGCAGCCC
fd040109r1    5-44   GGGGACTCATCGCGGTGGCGGCCGCTCTAGAAACTAGTGG
fd060109f1   18-30   ATTCCTGCAGCCC
fd060109r1   13-48   CCCGCGGTGGCGGCCGCTCTATACTAGTGGATTTTT
fd080109r1    7-44   GACTCCCCGCGGTGGCGGCCGCTCTAAACTAGTGGATT
fd100109r1    9-50   GACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTTTTC
fe040109f1    1-29   AAACCTTGGTATTCGAATTCCTGCAGCCC
fe050109r1    6-45   GACTCCCCGCGGTGGCGGCCGCTCTAGACTAGTGGGTCTT
fe090109r1   51-51   C
fe100109f1   26-26   C
fe100109r1    2-48   TGGGGGATTCCCCGCGGTGGCGGCCGCTCTACACTAGTGGATTCTCC
ff100109r1   15-49   CCCGCGGTGGCGGCCGCTCTAGACTAGTGGATTCT
fg020109f1   23-25   AAT
fg060109r1   65-65   C
fh010109f1    3-27   ACTTGTATTCGAATTCCTGCAGCCC
fh080109r1    7-45   GGGACTCCGCGCGGTGGCGGCCGCTCTANACTAGTGGAT

Near duplicate reads: 
aa090109f1            be080109f1      (imperfect: 14-935 (21)   5-922 (16) )
aa110109r1            ba090109r1      (imperfect: 24-942 (3)   18-941 (12) )
ab070109r1            bb070109r1      (imperfect: 21-960 (17)   17-961 (2) )
ac010109f1            bc010109f1      (imperfect: 20-945 (23)   15-930 (3) )
ac020109f1            cf020109f1      (imperfect: 13-952 (3)   11-954 (0) )
ac020109r1            cf020109r1      (imperfect: 21-949 (7)   17-955 (0) )
ac120109r1            ag060109r1      (imperfect: 7-940 (0)   7-941 (41) )
ad040109f1            fc020109f1      (imperfect: 34-946 (39)   42-955 (2) )
ae030109r1            ee050109r1      (imperfect: 15-971 (2)   13-974 (15) )
ae110109f1            bf060109r1      (imperfect: 45-936 (0)   49-940 (27) )
ae120109r1            bb120109r1      (imperfect: 15-934 (0)   8-925 (1) )
af020109f1            bc030109f1      (imperfect: 35-948 (0)   30-943 (7) )
af030109f1            cd050109f1      (imperfect: 34-968 (10)   39-978 (17) )
ag070109r1            dc100109r1      (imperfect: 12-957 (15)   6-968 (7) )
ah020109r1            df010109r1      (imperfect: 16-932 (10)   8-933 (5) )
ah090109r1            eh020109r1      (imperfect: 16-932 (21)   14-931 (1) )
ba040109f1            bd040109f1      (imperfect: 0-937 (5)   1-938 (28) )
bc070109f1            fd010109f1      (imperfect: 26-936 (0)   33-943 (3) )
bd060109f1            bf050109f1      (imperfect: 34-947 (5)   25-938 (0) )
bd060109r1            ef080109r1      (imperfect: 0-953 (33)   1-977 (10) )
bf040109r1            dc070109r1      (imperfect: 8-967 (0)   5-971 (0) )
bf120109r1            ed010109r1      (imperfect: 1-916 (0)   0-909 (44) )
bg040109f1            ca070109f1      (imperfect: 29-933 (7)   38-948 (5) )
ca050109f1            fb090109f1      (imperfect: 39-946 (1)   30-938 (20) )
ca050109f1            de120109r1      (imperfect: 39-923 (24)   48-933 (0) )
cb010109f1            fh010109f1      (imperfect: 3-909 (45)   2-903 (0) )
cb010109f1            dd040109f1      (imperfect: 9-954 (0)   8-950 (35) )
cb120109r1            fa100109r1      (imperfect: 35-925 (0)   43-931 (10) )
cc040109f1            de070109r1      (imperfect: 37-954 (15)   46-965 (15) )
ce060109f1            dc060109r1      (imperfect: 46-966 (1)   47-966 (10) )
cg100109f1            ec060109f1      (imperfect: 31-947 (2)   39-954 (0) )
ea010109f1            ec010109f1      (imperfect: 1-925 (4)   0-928 (8) )
ea120109f1            eb070109f1      (imperfect: 0-908 (1)   2-909 (47) )
eb050109f1            fd070109r1      (imperfect: 45-938 (2)   45-937 (27) )
ec120109f1            fc110109f1      (imperfect: 0-906 (0)   0-905 (28) )
ec120109r1            fc110109r1      (imperfect: 7-918 (6)   8-921 (14) )
ed060109f1            fd060109f1      (imperfect: 14-951 (2)   17-952 (33) )
ed060109r1            fd060109r1      (imperfect: 11-976 (0)   12-981 (3) )
ee020109f1            ff030109f1      (imperfect: 28-918 (2)   36-926 (36) )

Internal read matches (same orientation) : 
 42   aa070109r1    disjoint 60-mers  128-187 / 227-286 
 42   aa110109r1    disjoint 60-mers  600-659 / 699-758 
 35   ac060109f1    tandem (35-mer)_2    495-566 
253   ac070109f1    tandem (126-mer)_3     35-434 
140   ac070109f1    disjoint 148-mers  35-182 / 287-434 
602   ad050109f1    tandem (127-mer)_6     78-905 
498   ad050109f1    tandem (253-mer)_3     78-905 
370   ad050109f1    tandem (379-mer)_2     78-905 
254   ad050109f1    disjoint 323-mers  78-400 / 583-905 
141   ad050109f1    disjoint 197-mers  78-274 / 709-905 
 35   ae070109r1    tandem (36-mer)_4    347-520 
327   ae070109r1    tandem (126-mer)_4    446-974 
211   ae070109r1    tandem (252-mer)_2    446-974 
 35   af080109f1    tandem (36-mer)_4    179-352 
481   af080109f1    tandem (126-mer)_5    278-971 
374   af080109f1    tandem (252-mer)_2    278-971 
246   af080109f1    disjoint 318-mers  278-595 / 656-971 
130   af080109f1    disjoint 192-mers  278-469 / 782-971 
 38   af100109f1    tandem (42-mer)_2    621-708 
 42   ba090109r1    disjoint 60-mers  594-653 / 693-752 
520   bb040109f1    tandem (125-mer)_5     30-750 
416   bb040109f1    tandem (251-mer)_2     30-750 
285   bb040109f1    disjoint 343-mers  30-372 / 407-750 
169   bb040109f1    disjoint 217-mers  30-246 / 533-750 
 32   bc090109f1    tandem (37-mer)_2    841-923 
625   bc090109f1    tandem (126-mer)_6     88-914 
 35   bc090109f1    disjoint 53-mers  725-777 / 888-939 
521   bc090109f1    tandem (252-mer)_3     88-914 
393   bc090109f1    tandem (378-mer)_2     88-914 
277   bc090109f1    disjoint 324-mers  88-411 / 592-914 
164   bc090109f1    disjoint 198-mers  88-285 / 718-914 
 42   bc090109f1    disjoint 72-mers  88-159 / 844-914 
 35   bc090109f1    disjoint 53-mers  95-147 / 888-939 
 30   be090109f1    tandem (37-mer)_2    858-933 
 77   bh030109f1    tandem (93-mer)_2     48-242 
138   bh120109r1    tandem (126-mer)_2    580-916 
 38   ca030109r1    tandem (42-mer)_2    382-469 
 31   ca050109r1    tandem (36-mer)_4    200-373 
346   ca050109r1    tandem (126-mer)_4    299-890 
247   ca050109r1    tandem (252-mer)_2    299-921 
284   cg030109f1    tandem (127-mer)_3     30-478 
177   cg030109f1    disjoint 197-mers  30-226 / 283-478 
 55   cg030109f1    disjoint 71-mers  30-100 / 409-478 
131   cg030109r1    tandem (126-mer)_2    476-840 
 42   da030109r1    disjoint 60-mers  326-385 / 425-484 
 38   da110109r1    tandem (42-mer)_2    112-199 
 45   de020109r1    disjoint 60-mers  312-371 / 411-470 
 35   de120109f1    tandem (36-mer)_4    116-289 
508   de120109f1    tandem (126-mer)_5    215-921 
404   de120109f1    tandem (252-mer)_2    215-921 
273   de120109f1    disjoint 328-mers  215-542 / 593-921 
157   de120109f1    disjoint 202-mers  215-416 / 719-921 
 35   e0111p12sp6_f07  tandem (35-mer)_2    172-243 
567   eb050109r1    tandem (126-mer)_6    204-967 
463   eb050109r1    tandem (252-mer)_3    204-967 
341   eb050109r1    tandem (378-mer)_2    204-967 
219   eb050109r1    disjoint 263-mers  204-466 / 708-967 
106   eb050109r1    disjoint 137-mers  204-340 / 834-967 
389   ef030109r1    tandem (128-mer)_5    223-923 
330   ef030109r1    tandem (254-mer)_2    223-973 
221   ef030109r1    disjoint 372-mers  223-594 / 603-973 
 55   ef030109r1    disjoint 70-mers  223-292 / 853-923 
 35   eg010109f1    tandem (36-mer)_4    193-366 
396   eg010109f1    tandem (126-mer)_4    292-908 
280   eg010109f1    tandem (252-mer)_2    292-908 
162   eg010109f1    disjoint 234-mers  292-525 / 670-908 
 38   eg100109r1    tandem (42-mer)_2    499-586 
 35   fa040109f1    tandem (35-mer)_2    582-653 
 35   fa090109f1    tandem (35-mer)_2    611-682 
158   fb020109f1    tandem (126-mer)_2     28-325 
 42   fb020109f1    disjoint 46-mers  28-73 / 280-325 
 42   fb020109r1    disjoint 60-mers  523-582 / 622-681 
 34   fd070109f1    tandem (37-mer)_2    764-847 
607   fd070109f1    tandem (125-mer)_6     31-838 
 51   fd070109f1    disjoint 84-mers  648-731 / 811-894 
500   fd070109f1    tandem (251-mer)_3     31-838 
375   fd070109f1    tandem (377-mer)_2     31-838 
256   fd070109f1    disjoint 304-mers  31-334 / 534-838 
143   fd070109f1    disjoint 178-mers  31-208 / 660-838 
 38   fd070109f1    disjoint 68-mers  34-101 / 827-894 
 35   fd080109r1    tandem (36-mer)_4    210-383 
464   fd080109r1    tandem (126-mer)_5    309-965 
354   fd080109r1    tandem (252-mer)_2    309-965 
229   fd080109r1    disjoint 279-mers  309-587 / 687-965 
113   fd080109r1    disjoint 153-mers  309-461 / 813-965 
 38   fe110109r1    tandem (42-mer)_2    492-579 
 42   ff070109r1    disjoint 60-mers  338-397 / 437-496 
 35   ff100109f1    tandem (36-mer)_4    635-808 
384   fg100109r1    tandem (126-mer)_4    393-942 
277   fg100109r1    tandem (252-mer)_2    393-942 
158   fg100109r1    disjoint 172-mers  393-564 / 771-942 
 41   fg100109r1    disjoint 46-mers  393-438 / 897-942 
 42   fh020109r1    disjoint 60-mers  53-112 / 152-211 
404   fh070109r1    tandem (126-mer)_6     48-806 
325   fh070109r1    tandem (252-mer)_2     48-800 
201   fh070109r1    disjoint 364-mers  48-411 / 426-800 
 38   fh070109r1    disjoint 107-mers  53-159 / 688-800 
 38   fh120109r1    tandem (42-mer)_2    339-426 

No. of node-rejected pairs: 1.

Multi-segment reads (initially rejected segments in parentheses) -- XXX means segments flank X'd region: 
aa060109r1          (15 56)  55 960 
be020109r1          50 801  (816 948) 
bf050109r1          (9 51)  51 974 
bf080109r1          (9 45)  51 966 
bh120109r1          (2 45)  51 917 
ca050109r1          (8 45)  50 949 
cg030109r1          (11 46)  43 933 
db120109r1          (9 50)  52 939 
dd080109r1          (3 48)  48 979 
dd110109f1          20 371  (504 934) 
de120109r1          (11 45)  47 934 
dg080109r1          (1 47)  47 959 
ea060109r1          (9 50)  51 965 
eb050109r1          (2 45)  51 968 
eb060109r1          (9 50)  49 946 
eb080109r1          (9 50)  51 839 
ec050109r1          (7 48)  48 964 
ee120109r1          (6 44)  50 803 
ef030109r1          (14 49)  51 974 
fd040109r1          (5 44)  53 979 
fd080109r1          (7 44)  49 966 
fd100109r1          (9 50)  52 949 
fe100109r1          (2 48)  49 960 
ff100109r1          (15 49)  52 954 
fg110109r1          (56 190)  556 933 
fh080109r1          (7 45)  51 958 

26 reads with multiple segments.

Probable deletion reads (excluded from assembly):

ca050109r1    11    45- 50  (  fd080109r1     44- 60)

de120109r1    101    45- 47  (  ff100109r1     49-152)

eb050109r1    376    45- 51  (  bh120109r1     45-427)

ef030109r1    257    49- 51  (  cg030109r1     46-305)

4 probable deletion reads.


Revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90  615061  54.0  615061  54.0    0.00
 89    2046   0.2  617107  54.1    0.00
 88    2254   0.2  619361  54.3    0.00
 87    1869   0.2  621230  54.5    0.00
 86    1460   0.1  622690  54.6    0.00
 85    1809   0.2  624499  54.8    0.00
 84    1347   0.1  625846  54.9    0.00
 83    1421   0.1  627267  55.0    0.00
 82    1469   0.1  628736  55.2    0.00
 81    4400   0.4  633136  55.5    0.00
 80     849   0.1  633985  55.6    0.00
 79     586   0.1  634571  55.7    0.00
 78     571   0.1  635142  55.7    0.00
 77     655   0.1  635797  55.8    0.00
 76    1726   0.2  637523  55.9    0.00
 75     658   0.1  638181  56.0    0.00
 74     365   0.0  638546  56.0    0.00
 73     432   0.0  638978  56.1    0.00
 72     294   0.0  639272  56.1    0.00
 71     491   0.0  639763  56.1    0.00
 70     785   0.1  640548  56.2    0.00
 69     461   0.0  641009  56.2    0.00
 68     456   0.0  641465  56.3    0.00
 67     418   0.0  641883  56.3    0.00
 66   46422   4.1  688305  60.4    0.01
 65     731   0.1  689036  60.5    0.01
 64     221   0.0  689257  60.5    0.01
 63      69   0.0  689326  60.5    0.01
 62     258   0.0  689584  60.5    0.01
 61   20925   1.8  710509  62.3    0.03
 60    3251   0.3  713760  62.6    0.03
 59     483   0.0  714243  62.7    0.03
 58     513   0.0  714756  62.7    0.03
 57     680   0.1  715436  62.8    0.04
 56    4397   0.4  719833  63.2    0.05
 55    4640   0.4  724473  63.6    0.06
 54    2185   0.2  726658  63.8    0.07
 53    7551   0.7  734209  64.4    0.11
 52    3916   0.3  738125  64.8    0.13
 51    3042   0.3  741167  65.0    0.16
 50    2412   0.2  743579  65.2    0.18
 49     819   0.1  744398  65.3    0.19
 48    1047   0.1  745445  65.4    0.21
 47     844   0.1  746289  65.5    0.23
 46    1046   0.1  747335  65.6    0.25
 45    1537   0.1  748872  65.7    0.30
 44    1716   0.2  750588  65.9    0.37
 43    1616   0.1  752204  66.0    0.45
 42    2145   0.2  754349  66.2    0.58
 41    1505   0.1  755854  66.3    0.70
 40   20474   1.8  776328  68.1    2.75
 39     384   0.0  776712  68.1    2.80
 38     254   0.0  776966  68.2    2.84
 37     586   0.1  777552  68.2    2.96
 36     299   0.0  777851  68.2    3.03
 35     752   0.1  778603  68.3    3.27
 34     558   0.0  779161  68.4    3.49
 33     494   0.0  779655  68.4    3.74
 32     508   0.0  780163  68.4    4.06
 31     328   0.0  780491  68.5    4.32
 30     228   0.0  780719  68.5    4.55
 29     782   0.1  781501  68.6    5.53
 28     263   0.0  781764  68.6    5.95
 27     476   0.0  782240  68.6    6.90
 26     358   0.0  782598  68.7    7.80
 25    2615   0.2  785213  68.9   16.07
 24     588   0.1  785801  68.9   18.41
 23     459   0.0  786260  69.0   20.71
 22     368   0.0  786628  69.0   23.03
 21     434   0.0  787062  69.1   26.48
 20     445   0.0  787507  69.1   30.93
 19     738   0.1  788245  69.2   40.22
 18     289   0.0  788534  69.2   44.80
 17     386   0.0  788920  69.2   52.50
 16     633   0.1  789553  69.3   68.40
 15     654   0.1  790207  69.3   89.08
 14     537   0.0  790744  69.4  110.46
 13     749   0.1  791493  69.4  148.00
 12     653   0.1  792146  69.5  189.20
 11     981   0.1  793127  69.6  267.13
 10    1139   0.1  794266  69.7  381.03
  9    1503   0.1  795769  69.8  570.24
  8     797   0.1  796566  69.9  696.56
  7     813   0.1  797379  70.0  858.77
  6     362   0.0  797741  70.0  949.70
  5      26   0.0  797767  70.0  957.93
  4     100   0.0  797867  70.0  997.74
  3      29   0.0  797896  70.0  1012.27
  2  174015  15.3  971911  85.3  110808.31
  0   10330   0.9  982241  86.2  121138.31
 -1  157580  13.8  1139821 100.0  278718.31   (quality -1 = terminal quality 0)

Avg. full length: 987.7, trimmed (qual > -1): 851.2
Avg. quality: 57.8 per base

LLR score histogram:
Score    #   cum # 
-95.0  5009  5009
-90.0   174  5183
-85.0    96  5279
-80.0    47  5326
-75.0    65  5391
-70.0    60  5451
-65.0    42  5493
-60.0   101  5594
-55.0    76  5670
-50.0    48  5718
-45.0    43  5761
-40.0    90  5851
-35.0    50  5901
-30.0    70  5971
-25.0    84  6055
-20.0    56  6111
-15.0    53  6164
-10.0    77  6241
 -5.0   109  6350
  0.0  3452  9802
  5.0  3786  13588
 10.0  3352  16940
 15.0  2366  19306
 20.0    28  19334

LLR score histogram:
Score    #   cum # 
-95.0  4954  4954
-90.0   202  5156
-85.0    90  5246
-80.0    68  5314
-75.0    59  5373
-70.0    63  5436
-65.0    46  5482
-60.0    84  5566
-55.0    80  5646
-50.0    58  5704
-45.0    39  5743
-40.0    66  5809
-35.0    66  5875
-30.0    65  5940
-25.0    72  6012
-20.0    58  6070
-15.0    67  6137
-10.0    55  6192
 -5.0   105  6297
  0.0  3387  9684
  5.0  3770  13454
 10.0  3401  16855
 15.0  2450  19305
 20.0    29  19334

2d revised quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90  607012  53.3  607012  53.3    0.00
 89    2113   0.2  609125  53.4    0.00
 88    2422   0.2  611547  53.7    0.00
 87    1864   0.2  613411  53.8    0.00
 86    1560   0.1  614971  54.0    0.00
 85    1996   0.2  616967  54.1    0.00
 84    1488   0.1  618455  54.3    0.00
 83    1384   0.1  619839  54.4    0.00
 82    1527   0.1  621366  54.5    0.00
 81    4137   0.4  625503  54.9    0.00
 80     891   0.1  626394  55.0    0.00
 79     695   0.1  627089  55.0    0.00
 78     594   0.1  627683  55.1    0.00
 77     685   0.1  628368  55.1    0.00
 76    1472   0.1  629840  55.3    0.00
 75     699   0.1  630539  55.3    0.00
 74     404   0.0  630943  55.4    0.00
 73     458   0.0  631401  55.4    0.00
 72     335   0.0  631736  55.4    0.00
 71     475   0.0  632211  55.5    0.00
 70     674   0.1  632885  55.5    0.00
 69     402   0.0  633287  55.6    0.00
 68     362   0.0  633649  55.6    0.00
 67     352   0.0  634001  55.6    0.00
 66   50125   4.4  684126  60.0    0.01
 65     712   0.1  684838  60.1    0.01
 64     238   0.0  685076  60.1    0.01
 63      88   0.0  685164  60.1    0.01
 62     259   0.0  685423  60.1    0.01
 61   22183   1.9  707606  62.1    0.03
 60    3398   0.3  711004  62.4    0.04
 59     477   0.0  711481  62.4    0.04
 58     521   0.0  712002  62.5    0.04
 57     676   0.1  712678  62.5    0.04
 56    4642   0.4  717320  62.9    0.05
 55    5089   0.4  722409  63.4    0.07
 54    2317   0.2  724726  63.6    0.08
 53    8082   0.7  732808  64.3    0.12
 52    4139   0.4  736947  64.7    0.14
 51    3230   0.3  740177  64.9    0.17
 50    2544   0.2  742721  65.2    0.19
 49     843   0.1  743564  65.2    0.20
 48    1077   0.1  744641  65.3    0.22
 47     883   0.1  745524  65.4    0.24
 46    1059   0.1  746583  65.5    0.26
 45    1580   0.1  748163  65.6    0.31
 44    1729   0.2  749892  65.8    0.38
 43    1622   0.1  751514  65.9    0.46
 42    2168   0.2  753682  66.1    0.60
 41    1503   0.1  755185  66.3    0.72
 40   20211   1.8  775396  68.0    2.74
 39     409   0.0  775805  68.1    2.79
 38     283   0.0  776088  68.1    2.84
 37     619   0.1  776707  68.1    2.96
 36     316   0.0  777023  68.2    3.04
 35     789   0.1  777812  68.2    3.29
 34     573   0.1  778385  68.3    3.52
 33     510   0.0  778895  68.3    3.77
 32     530   0.0  779425  68.4    4.11
 31     348   0.0  779773  68.4    4.39
 30     239   0.0  780012  68.4    4.62
 29     805   0.1  780817  68.5    5.64
 28     305   0.0  781122  68.5    6.12
 27     501   0.0  781623  68.6    7.12
 26     377   0.0  782000  68.6    8.07
 25    2726   0.2  784726  68.8   16.69
 24     615   0.1  785341  68.9   19.14
 23     470   0.0  785811  68.9   21.49
 22     378   0.0  786189  69.0   23.88
 21     441   0.0  786630  69.0   27.38
 20     476   0.0  787106  69.1   32.14
 19     758   0.1  787864  69.1   41.68
 18     299   0.0  788163  69.1   46.42
 17     395   0.0  788558  69.2   54.30
 16     651   0.1  789209  69.2   70.66
 15     660   0.1  789869  69.3   91.53
 14     538   0.0  790407  69.3  112.94
 13     781   0.1  791188  69.4  152.09
 12     676   0.1  791864  69.5  194.74
 11     985   0.1  792849  69.6  272.98
 10    1114   0.1  793963  69.7  384.38
  9    1575   0.1  795538  69.8  582.66
  8     770   0.1  796308  69.9  704.70
  7     962   0.1  797270  69.9  896.64
  6     353   0.0  797623  70.0  985.31
  5     276   0.0  797899  70.0  1072.59
  4     408   0.0  798307  70.0  1235.02
  3     206   0.0  798513  70.1  1338.26
  2  173398  15.2  971911  85.3  110745.01
  0   10330   0.9  982241  86.2  121075.01
 -1  157580  13.8  1139821 100.0  278655.01   (quality -1 = terminal quality 0)

Avg. full length: 987.7, trimmed (qual > -1): 851.2
Avg. quality: 57.6 per base

No. confirmed reads: 982
Avg. length: 957.4, confirmed: 841.7, str. confirmed: 746.1, trimmed: 857.9
Preliminary clone size estimate: 67062 bp, depth of coverage: 12.3

Depth histogram (max_depth, #reads, cum #reads):

25   109     109
24    12     121
23    87     208
22    73     281
21    65     346
20    20     366
19    40     406
18    59     465
17    51     516
16    54     570
15    52     622
14    54     676
13    56     732
12    33     765
11    48     813
10    22     835
 9    37     872
 8    32     904
 7    16     920
 6    28     948
 5    15     963
 4    13     976
 3     3     979
 2     3     982
 0   168     1150

Forward confirmed bases: 0

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      0      0      0      0      0      0        0
C      0      0      0      0      0      0      0        0
G      0      0      0      0      0      0      0        0
T      0      0      0      0      0      0      0        0
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
       Total

Histogram of spacings between adjacent indel pairs:


Reverse confirmed bases: 0

Substitutions by nucleotide:
       A      C      G      T      N      X      Z    Total
A      0      0      0      0      0      0      0        0
C      0      0      0      0      0      0      0        0
G      0      0      0      0      0      0      0        0
T      0      0      0      0      0      0      0        0
N      0      0      0      0      0      0      0        0
X      0      0      0      0      0      0      0        0
Z      0      0      0      0      0      0      0        0

Substitutions by quality: 
       Total

Histogram of spacings between adjacent indel pairs:


Blocked reads: 
ae090109r1 158 284   right
ae100109f1 49 764   right
ae100109r1 597 838   right
ae120109f1 80 897  left 
af040109f1 27 651   right
af100109f1 41 816  left 
ag120109f1 19 601  left 
ag120109r1 55 637   right
bb020109f1 80 738  left 
bc070109r1 75 863  left 
be020109r1 49 847   right
bf020109r1 80 695  left 
bh030109f1 80 815   right
cb050109r1 99 645  left 
dd120109r1 666 699  left 
ee100109r1 80 830  left 
eh020109r1 17 791  left 
fc030109r1 80 819  left 
fc060109r1 80 807  left 
fc120109r1 48 628   right
fd010109r1 51 835  left 
fg110109r1 88 721  left 
fh050109f1 80 812  left 

23 blocked reads: 15 left only, 8 right only, 0 both.
23 reads (not shown) lack a high-quality segment.
Bypassed reads: cd060109r1 

0 perfect duplicates

164 isolated singletons (having no non-vector match to any other read): 
  Read         Length      (# trimmed non-X bases)
 df120109f1     919   (0)
 dg010109f1    1169   (0)
 dg020109f1    1119   (0)
 dg020109r1    1733   (0)
 df100109f1    1021   (0)
 df040109r1    2463   (0)
 df050109f1    1262   (0)
 df060109f1    1013   (0)
 df070109f1     965   (0)
 dg040109f1     981   (0)
 dg100109r1     959   (0)
 dg110109r1     931   (0)
 dg120109f1    1042   (0)
 dh010109f1    1529   (0)
 dg100109f1     954   (0)
 dg050109f1     976   (0)
 dg060109f1     966   (0)
 dg070109f1     980   (0)
 dg070109r1     977   (814)
 dg090109f1     979   (0)
 df040109f1    1070   (0)
 dc070109f1     965   (0)
 dc080109f1    1019   (0)
 dc090109f1     931   (0)
 dc100109f1     974   (0)
 dc060109f1     980   (0)
 dc020109f1    1237   (0)
 dc030109f1     992   (0)
 dc030109r1    1424   (0)
 dc040109r1    2108   (0)
 dc050109r1     957   (0)
 dc110109f1    1121   (0)
 de030109r1    1753   (0)
 de100109f1    1014   (0)
 de100109r1    2189   (0)
 df020109f1     958   (0)
 dd090109f1     967   (0)
 dc110109r1     957   (0)
 dc120109f1     925   (0)
 dd010109f1     949   (0)
 dd010109r1     987   (0)
 dd030109r1    2202   (0)
 dh020109f1     925   (0)
 fa110109f1     935   (0)
 fa120109f1     923   (0)
 fa120109r1     936   (0)
 fb080109f1    1400   (0)
 fa090109r1     943   (0)
 fa020109r1     942   (771)
 fa040109r1     957   (0)
 fa070109f1    2154   (0)
 fa070109r1    2211   (0)
 fb080109r1    1220   (0)
 fg120109f1     920   (782)
 fg120109r1     913   (763)
 fh090109f1    1560   (0)
 fh090109r1    2123   (0)
 ff090109f1     979   (0)
 fc080109f1    1922   (0)
 fc080109r1    1750   (0)
 ff020109f1     955   (0)
 ff020109r1     947   (0)
 ff040109f1     958   (0)
 fa020109f1     949   (735)
 dh070109f1     920   (0)
 dh110109f1     921   (0)
 dh120109f1     925   (0)
 dh120109r1     922   (0)
 dh060109f1     973   (0)
 dh030109f1     965   (0)
 dh040109f1     962   (0)
 dh040109r1     961   (0)
 dh050109f1    1026   (0)
 dh050109r1     964   (0)
 e0111p12t7_c07  1662   (0)
 ef010109f1     923   (776)
 ef010109r1     938   (668)
 ef100109f1     943   (0)
 ef100109r1     957   (0)
 ee040109r1     996   (0)
 ea020109f1     921   (0)
 eb120109r1     936   (26)
 ed070109r1    1927   (0)
 ed120109f1     908   (0)
 ed120109r1     929   (0)
 dc050109f1    1075   (0)
 cb020109f1     949   (0)
 cb020109r1     958   (0)
 cb060109f1     957   (0)
 cb060109r1    1027   (0)
 ca100109r1    1639   (0)
 ca060109f1     955   (0)
 ca060109r1     964   (0)
 ca080109f1    1031   (0)
 ca080109r1    1498   (0)
 cb100109f1     938   (0)
 ce040109r1    1301   (0)
 ce050109r1    1241   (0)
 ce080109r1    1965   (0)
 ce110109f1     936   (738)
 cd070109r1    2234   (0)
 cb110109f1     939   (786)
 cb110109r1     941   (703)
 cc080109f1    1587   (0)
 cd050109r1    2532   (0)
 bh070109r1    1480   (0)
 ag110109r1     949   (0)
 ah050109f1    1068   (0)
 ah050109r1    1752   (0)
 ba060109f1     945   (0)
 ag110109f1    1030   (0)
 ab120109f1     933   (0)
 ad100109f1     998   (0)
 ad100109r1     983   (0)
 ae090109f1     968   (0)
 ba060109r1     982   (0)
 bb060109r1    2275   (0)
 bh030109f1     939   (735)
 bh030109r1     954   (738)
 bh070109f1     942   (0)
 bb060109f1    2153   (0)
 ba080109f1     968   (0)
 ba080109r1     994   (0)
 bb010109f1     940   (0)
 bb010109r1     954   (0)
 cc080109r1    2130   (0)
 db010109f1     981   (0)
 db010109r1     973   (0)
 db020109f1     978   (0)
 db030109f1     995   (0)
 da120109r1     933   (0)
 da070109f1     956   (0)
 da080109f1    1159   (0)
 da110109f1     943   (0)
 da120109f1    1052   (0)
 db040109f1    1511   (0)
 db100109f1     946   (0)
 db110109f1     943   (0)
 db120109f1    1091   (0)
 dc010109f1    1106   (0)
 db090109f1     983   (0)
 db040109r1    1901   (0)
 db050109f1     984   (0)
 db060109f1     976   (0)
 db070109f1     989   (0)
 db080109f1    1018   (0)
 da090109f1    1079   (0)
 da010109f1     947   (0)
 da020109f1    1224   (0)
 cf050109r1    2320   (0)
 da030109f1    1223   (0)
 cf060109r1    1209   (0)
 cf080109f1     969   (0)
 cg020109r1     943   (0)
 cg060109f1    1315   (0)
 cg060109r1    1565   (0)
 cg120109f1     928   (0)
 da040109f1    1289   (0)
 ch030109r1    1010   (0)
 da060109f1     957   (0)
 ce110109r1     936   (708)
 cf030109r1    1014   (0)
 cf030109f1     970   (0)
 da050109f1    1016   (0)

Contig 1.  1 read; 958 bp (untrimmed), 558 (trimmed).
 ****  PROBABLE DELETION READ
      1   958 ca050109r1    945 (748)  0.00 0.00 0.00    0 (958)    0 (957) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56       8   0.8       8   0.8    0.00
 50       6   0.6      14   1.5    0.00
 48       1   0.1      15   1.6    0.00
 47       5   0.5      20   2.1    0.00
 46       1   0.1      21   2.2    0.00
 44      58   6.1      79   8.2    0.00
 43       1   0.1      80   8.4    0.00
 42      73   7.6     153  16.0    0.01
 40      13   1.4     166  17.3    0.01
 39       4   0.4     170  17.7    0.01
 38       2   0.2     172  18.0    0.01
 37      44   4.6     216  22.5    0.02
 36       6   0.6     222  23.2    0.02
 35      47   4.9     269  28.1    0.03
 34       9   0.9     278  29.0    0.04
 33      23   2.4     301  31.4    0.05
 32      18   1.9     319  33.3    0.06
 31      10   1.0     329  34.3    0.07
 30      25   2.6     354  37.0    0.09
 29      20   2.1     374  39.0    0.12
 28      10   1.0     384  40.1    0.13
 27      11   1.1     395  41.2    0.16
 26       4   0.4     399  41.6    0.17
 25       9   0.9     408  42.6    0.20
 24      14   1.5     422  44.1    0.25
 23      10   1.0     432  45.1    0.30
 22      19   2.0     451  47.1    0.42
 21       5   0.5     456  47.6    0.46
 20       9   0.9     465  48.5    0.55
 19      13   1.4     478  49.9    0.71
 18       9   0.9     487  50.8    0.86
 17       3   0.3     490  51.1    0.92
 16       9   0.9     499  52.1    1.14
 15       5   0.5     504  52.6    1.30
 14      11   1.1     515  53.8    1.74
 13       6   0.6     521  54.4    2.04
 12       7   0.7     528  55.1    2.48
 11      16   1.7     544  56.8    3.75
 10      10   1.0     554  57.8    4.75
  9       2   0.2     556  58.0    5.00
  8       2   0.2     558  58.2    5.32
 -1     400  41.8     958 100.0  405.32   (quality -1 = terminal quality 0)

Avg. full length: 958.0, trimmed (qual > -1): 558.0
Avg. quality: 18.5 per base

Initial, terminal qual 0 segments:  1-97, 656-958

Regions of LLR- adjusted quality < 2.0:
1-97, 129-131, 147-150, 267-268, 302-311, 324, 359-361, 481-485, 
507-509, 538-540, 545-554, 562-569, 573-574, 578-583, 587-591, 601-611, 
619-622, 628-630, 634, 642-648, 654-958, 

21 regions, avg size 23.5, avg spacing 45.6

First_start: 958, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  958 [12.4] (0,0)     ca050109r1         1-958 | (8 45)  50 949 | DA:(**50 949**) || local(+/-) (0.0,0.0), distant (17.1,0.0)

Gaps in unique-read coverage:  None.

Contig 2.  1 read; 934 bp (untrimmed), 757 (trimmed).
 ****  PROBABLE DELETION READ
      1   934 de120109r1    920 (831)  0.00 0.00 0.00    0 (934)    0 (933) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     109  11.7     109  11.7    0.00
 51      26   2.8     135  14.5    0.00
 50      39   4.2     174  18.6    0.00
 48       1   0.1     175  18.7    0.00
 47       6   0.6     181  19.4    0.00
 46      10   1.1     191  20.4    0.00
 45       8   0.9     199  21.3    0.00
 44      25   2.7     224  24.0    0.00
 43      53   5.7     277  29.7    0.01
 42      90   9.6     367  39.3    0.01
 41      31   3.3     398  42.6    0.01
 40      75   8.0     473  50.6    0.02
 39       1   0.1     474  50.7    0.02
 38      12   1.3     486  52.0    0.02
 37      23   2.5     509  54.5    0.03
 36       4   0.4     513  54.9    0.03
 35      57   6.1     570  61.0    0.05
 34      10   1.1     580  62.1    0.05
 33      16   1.7     596  63.8    0.06
 32      11   1.2     607  65.0    0.07
 31       8   0.9     615  65.8    0.07
 30       7   0.7     622  66.6    0.08
 29      15   1.6     637  68.2    0.10
 28       7   0.7     644  69.0    0.11
 27      15   1.6     659  70.6    0.14
 26       2   0.2     661  70.8    0.14
 25       8   0.9     669  71.6    0.17
 24       9   1.0     678  72.6    0.20
 23       8   0.9     686  73.4    0.24
 22      10   1.1     696  74.5    0.31
 21       7   0.7     703  75.3    0.36
 20      13   1.4     716  76.7    0.49
 19      10   1.1     726  77.7    0.62
 18       2   0.2     728  77.9    0.65
 17       7   0.7     735  78.7    0.79
 15       6   0.6     741  79.3    0.98
 14       3   0.3     744  79.7    1.10
 13       1   0.1     745  79.8    1.15
 12       3   0.3     748  80.1    1.34
 11       2   0.2     750  80.3    1.50
 10       7   0.7     757  81.0    2.20
 -1     177  19.0     934 100.0  179.20   (quality -1 = terminal quality 0)

Avg. full length: 934.0, trimmed (qual > -1): 757.0
Avg. quality: 32.2 per base

Initial, terminal qual 0 segments:  1-48, 806-934

Regions of LLR- adjusted quality < 2.0:
1-48, 56-61, 654-655, 690, 695-697, 717-722, 744-749, 759-760, 
775-781, 785-790, 796, 798, 806-934, 

13 regions, avg size 16.8, avg spacing 71.8

First_start: 934, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  934 [16.8] (0,0)     de120109r1         1-934 | (11 45)  47 934 | DA:(**47 934**) || local(+/-) (0.0,0.0), distant (19.4,0.0)

Gaps in unique-read coverage:  None.

Contig 3.  1 read; 968 bp (untrimmed), 759 (trimmed).
 ****  PROBABLE DELETION READ
      1   968 eb050109r1    961 (786)  0.00 0.00 0.00    0 (968)    0 (967) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 56     115  11.9     115  11.9    0.00
 51      96   9.9     211  21.8    0.00
 50      17   1.8     228  23.6    0.00
 48       3   0.3     231  23.9    0.00
 47       2   0.2     233  24.1    0.00
 46      10   1.0     243  25.1    0.00
 45      18   1.9     261  27.0    0.00
 44      22   2.3     283  29.2    0.00
 43      91   9.4     374  38.6    0.01
 42      77   8.0     451  46.6    0.01
 41      19   2.0     470  48.6    0.01
 40      65   6.7     535  55.3    0.02
 39       2   0.2     537  55.5    0.02
 38      11   1.1     548  56.6    0.02
 37       8   0.8     556  57.4    0.02
 36       2   0.2     558  57.6    0.02
 35      34   3.5     592  61.2    0.04
 34       3   0.3     595  61.5    0.04
 33       8   0.8     603  62.3    0.04
 32      12   1.2     615  63.5    0.05
 31      13   1.3     628  64.9    0.06
 30       1   0.1     629  65.0    0.06
 29      16   1.7     645  66.6    0.08
 28       7   0.7     652  67.4    0.09
 27       7   0.7     659  68.1    0.10
 26       5   0.5     664  68.6    0.12
 25      10   1.0     674  69.6    0.15
 24      17   1.8     691  71.4    0.22
 23       6   0.6     697  72.0    0.25
 22       5   0.5     702  72.5    0.28
 21      10   1.0     712  73.6    0.36
 20       2   0.2     714  73.8    0.38
 19       9   0.9     723  74.7    0.49
 18       5   0.5     728  75.2    0.57
 17       4   0.4     732  75.6    0.65
 16       2   0.2     734  75.8    0.70
 15       6   0.6     740  76.4    0.89
 14       2   0.2     742  76.7    0.97
 13       5   0.5     747  77.2    1.22
 12       2   0.2     749  77.4    1.35
 11       2   0.2     751  77.6    1.51
 10       2   0.2     753  77.8    1.71
  9       6   0.6     759  78.4    2.46
 -1     209  21.6     968 100.0  211.46   (quality -1 = terminal quality 0)

Avg. full length: 968.0, trimmed (qual > -1): 759.0
Avg. quality: 32.3 per base

Initial, terminal qual 0 segments:  1-50, 810-968

Regions of LLR- adjusted quality < 2.0:
1-51, 59-64, 639-640, 709-710, 728-729, 746, 762-774, 783-790, 
795, 797-803, 808-968, 

11 regions, avg size 23.1, avg spacing 88.0

First_start: 968, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  968 [16.9] (0,0)     eb050109r1         1-968 | (2 45)  51 968 | DA:(**51 968**) || local(+/-) (0.0,0.0), distant (17.9,0.0)

Gaps in unique-read coverage:  None.

Contig 4.  1 read; 974 bp (untrimmed), 528 (trimmed).
 ****  PROBABLE DELETION READ
      1   974 ef030109r1    961 (635)  0.10 0.00 0.00    0 (974)    0 (973) 

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 46       3   0.3       3   0.3    0.00
 42       5   0.5       8   0.8    0.00
 39       3   0.3      11   1.1    0.00
 37       9   0.9      20   2.1    0.00
 36       1   0.1      21   2.2    0.00
 35       5   0.5      26   2.7    0.00
 33      17   1.7      43   4.4    0.01
 32       2   0.2      45   4.6    0.01
 31      10   1.0      55   5.6    0.02
 30      15   1.5      70   7.2    0.04
 29      14   1.4      84   8.6    0.05
 28      14   1.4      98  10.1    0.08
 27      25   2.6     123  12.6    0.13
 26      10   1.0     133  13.7    0.15
 25      21   2.2     154  15.8    0.22
 24      14   1.4     168  17.2    0.27
 23      34   3.5     202  20.7    0.44
 22      20   2.1     222  22.8    0.57
 21      26   2.7     248  25.5    0.78
 20      14   1.4     262  26.9    0.92
 19      39   4.0     301  30.9    1.41
 18      15   1.5     316  32.4    1.65
 17      12   1.2     328  33.7    1.89
 16      34   3.5     362  37.2    2.74
 15      27   2.8     389  39.9    3.59
 14      17   1.7     406  41.7    4.27
 13      29   3.0     435  44.7    5.72
 12      21   2.2     456  46.8    7.05
 11      41   4.2     497  51.0   10.31
 10      13   1.3     510  52.4   11.61
  9      10   1.0     520  53.4   12.86
  8       4   0.4     524  53.8   13.50
  7       2   0.2     526  54.0   13.90
  6       2   0.2     528  54.2   14.40
 -1     446  45.8     974 100.0  460.40   (quality -1 = terminal quality 0)

Avg. full length: 974.0, trimmed (qual > -1): 528.0
Avg. quality: 11.1 per base

Initial, terminal qual 0 segments:  1-66, 595-974

Regions of LLR- adjusted quality < 2.0:
1-66, 78-89, 93-105, 107-110, 112, 118-120, 122-132, 135-141, 
143-148, 154-158, 160, 172-175, 192-197, 200-204, 208-210, 215, 
217-219, 248-250, 256-258, 265-269, 274-280, 293-297, 300-303, 313-315, 
319-321, 326-335, 337-338, 341-351, 354-356, 359-362, 364, 367-371, 
377-379, 384-390, 392, 401-407, 413-414, 416, 422-426, 431-433, 
439-444, 453-457, 461-464, 470-474, 476, 484-485, 490-504, 510-511, 
513-515, 517, 525-533, 535-537, 539, 545, 547-551, 553, 
557-559, 564-570, 578, 581-585, 588-590, 595-974, 

62 regions, avg size 11.5, avg spacing 15.7

First_start: 974, last_end: 1

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  974 [11.7] (0,0)     ef030109r1         1-974 | (14 49)  51 974 | DA:(**51 974**) || local(+/-) (0.0,0.0), distant (16.6,0.0)

Gaps in unique-read coverage:  None.

Contig 5.  2 reads; 43 bp (untrimmed), 0 (trimmed).  Isolated contig.
    -11   922 ab120109r1     41 (  0)  0.00 0.00 0.00   12 ( 12)  879 (879) 
    -10   949 ab100109r1     38 (  0)  2.33 0.00 0.00   11 ( 11)  906 (906) 

Overall discrep rates (%):             1.16 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      43 100.0      43 100.0   43.00   (quality -1 = terminal quality 0)

Avg. full length: 43.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-43, (None)

Regions of LLR- adjusted quality < 2.0:
1-43, 

1 regions, avg size 43.0, avg spacing 43.0

First_start: 1, last_end: 43

Slack, # used pairs (max_score), unused
 0     1  ( 0.0)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
   44 - right        0+      ab100109r1   ( -10)    No             53+

Bottom strand: 
 left - right       43+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
37      2      2     86 (100.00)     0  0    0   0   0   0     0 (0.00)    0    1 (1.16)
34      1      3     84 ( 97.67)     0  0    0   0   0   0     0 (0.00)    0    1 (1.19)
32      2      5     83 ( 96.51)     0  0    0   0   0   0     0 (0.00)    0    1 (1.20)
31      2      7     81 ( 94.19)     0  0    0   0   0   0     0 (0.00)    0    1 (1.23)
29      7     14     79 ( 91.86)     0  0    0   0   0   0     0 (0.00)    0    1 (1.27)
27      6     20     72 ( 83.72)     0  0    0   0   0   0     0 (0.00)    0    1 (1.39)
25      1     21     66 ( 76.74)     0  0    0   0   0   0     0 (0.00)    0    1 (1.52)
24      1     22     65 ( 75.58)     0  0    0   0   0   0     0 (0.00)    0    1 (1.54)
23      3     25     64 ( 74.42)     0  0    0   0   0   0     0 (0.00)    0    1 (1.56)
22      6     31     61 ( 70.93)     0  0    0   0   0   0     0 (0.00)    0    1 (1.64)
20      4     35     55 ( 63.95)     0  0    0   0   0   0     0 (0.00)    0    1 (1.82)
19      2     37     51 ( 59.30)     0  0    0   0   0   0     0 (0.00)    0    1 (1.96)
16      7     44     49 ( 56.98)     0  0    0   0   0   0     0 (0.00)    0    1 (2.04)
15      2     46     42 ( 48.84)     0  0    0   0   0   0     0 (0.00)    0    1 (2.38)
14      3     49     40 ( 46.51)     0  0    0   0   0   0     0 (0.00)    0    1 (2.50)
13      3     52     37 ( 43.02)     0  0    0   0   0   0     0 (0.00)    0    1 (2.70)
11      1     53     34 ( 39.53)     0  0    0   0   0   0     0 (0.00)    0    1 (2.94)
10      5     58     33 ( 38.37)     0  0    0   0   0   0     0 (0.00)    0    1 (3.03)
 9     11     69     28 ( 32.56)     0  0    0   0   0   0     0 (0.00)    0    1 (3.57)
 7     11     80     17 ( 19.77)     0  0    0   0   0   0     0 (0.00)    0    1 (5.88)
 6      3     83      6 (  6.98)     0  0    0   0   0   0     0 (0.00)    0    1 (16.67)
 4      3     86      3 (  3.49)     0  0    0   1   0   0     1 (33.33)    1    1 (33.33)
-1      0     86      0 (  0.00)     0  0    0   0   0   0     0 (0.00)    1    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
-1     86     86      0 (  0.00)     0  0    0   1   0   0     1 (1.16)    1    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      43       43        1

SS region: 43 (100.00%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
    28  S     ab100109r1      (0)/(0)  27 ACA / ATA

0 HQ discrepancies in 0 reads.
1 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 6.  2 reads; 47 bp (untrimmed), 0 (trimmed).  Isolated contig.
     -1   929 fa110109r1     31 (  0)  2.86 0.00 0.00   14 ( 14)  882 (882) 
      1   949 ea020109r1     46 (  0)  0.00 0.00 0.00    0 ( 12)  902 (902) 

Overall discrep rates (%):             1.22 0.00 0.00

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 -1      47 100.0      47 100.0   47.00   (quality -1 = terminal quality 0)

Avg. full length: 47.0, trimmed (qual > -1): 0.0
Avg. quality: 0.0 per base

Initial, terminal qual 0 segments:  1-47, (None)

Regions of LLR- adjusted quality < 2.0:
1-47, 

1 regions, avg size 47.0, avg spacing 47.0

First_start: 13, last_end: 47

Slack, # used pairs (max_score), unused
 0     1  ( 0.0)     0 ( 0.0)        1

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
   48 - right        0+      ea020109r1   (   1)    No             46+

Bottom strand: 
 left - right       47+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
33      1      1     70 (100.00)     0  0    0   0   0   0     0 (0.00)    0    1 (1.43)
29     15     16     69 ( 98.57)     0  0    0   0   0   0     0 (0.00)    0    1 (1.45)
28      1     17     54 ( 77.14)     0  0    0   0   0   0     0 (0.00)    0    1 (1.85)
27      3     20     53 ( 75.71)     0  0    0   0   0   0     0 (0.00)    0    1 (1.89)
26      2     22     50 ( 71.43)     0  0    0   0   0   0     0 (0.00)    0    1 (2.00)
25      2     24     48 ( 68.57)     0  0    0   0   0   0     0 (0.00)    0    1 (2.08)
22      2     26     46 ( 65.71)     0  0    0   0   0   0     0 (0.00)    0    1 (2.17)
20      1     27     44 ( 62.86)     0  0    0   0   0   0     0 (0.00)    0    1 (2.27)
19      3     30     43 ( 61.43)     0  0    0   0   0   0     0 (0.00)    0    1 (2.33)
17      2     32     40 ( 57.14)     0  0    0   0   0   0     0 (0.00)    0    1 (2.50)
16      4     36     38 ( 54.29)     0  0    0   0   0   0     0 (0.00)    0    1 (2.63)
15      2     38     34 ( 48.57)     0  0    0   0   0   0     0 (0.00)    0    1 (2.94)
14      2     40     32 ( 45.71)     0  0    0   0   0   0     0 (0.00)    0    1 (3.12)
13      5     45     30 ( 42.86)     0  0    0   0   0   0     0 (0.00)    0    1 (3.33)
11      1     46     25 ( 35.71)     0  0    0   0   0   0     0 (0.00)    0    1 (4.00)
10      2     48     24 ( 34.29)     0  0    0   0   0   0     0 (0.00)    0    1 (4.17)
 9      6     54     22 ( 31.43)     0  0    0   1   0   0     1 (16.67)    1    1 (4.55)
 8      8     62     16 ( 22.86)     0  0    0   0   0   0     0 (0.00)    1    0 (0.00)
 7      3     65      8 ( 11.43)     0  0    0   0   0   0     0 (0.00)    1    0 (0.00)
 6      5     70      5 (  7.14)     0  0    0   0   0   0     0 (0.00)    1    0 (0.00)
-1     12     82      0 (  0.00)    12  0    0   0   0   0     0 (0.00)    1    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
-1     82     82      0 (  0.00)    12  0    0   1   0   0     1 (1.22)    1    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      47       47        1

SS region: 47 (100.00%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality):
    33  S     fa110109r1      (0)/(0)  32 AGA / ACA

0 HQ discrepancies in 0 reads.
1 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 7.  20 reads; 4291 bp (untrimmed), 4112 (trimmed).  Isolated contig.
      1   943 fh050109f1    830 (  0)  0.00 0.11 0.00    0 (396)    0 (  0) 
    347  1280 ed100109r1    740 (  0)  0.23 0.11 0.23   50 ( 50)    0 ( 11) 
    459  1431 eb040109r1    789 (  0)  0.11 0.11 0.00   49 ( 49)    0 (  0) 
    945  1863 ce120109r1    727 (  0)  1.26 0.11 0.23   48 ( 48)    0 (  0) 
   1106  2039 ff110109r1    776 (  0)  0.34 0.11 0.00   53 ( 53)    1 (  1) 
   1176  2083 ch010109r1    693 (  0)  1.99 0.00 0.23   52 ( 52)    3 (  8) 
   1512  2466 bd050109f1    787 (  0)  2.05 0.32 0.00   29 ( 29)    0 (  0) 
C  1536  2489 fh050109r1    756 (  0)  1.33 1.22 0.00    4 (  4)   48 ( 48) 
   1859  2827 fc030109f1    854 (  0)  0.11 0.21 0.00   31 ( 31)    0 (  0) 
   1922  2898 cb050109f1    841 (  0)  0.53 0.00 0.21   32 ( 32)    0 (  0) 
C  2021  2945 ed100109f1    671 (  0)  3.46 0.89 0.33    1 ( 60)   27 ( 27) 
   2048  3008 ag100109f1    838 (  0)  0.22 0.00 0.00   35 ( 35)    1 (  1) 
C  2141  3075 eb040109f1    728 (  0)  1.67 1.00 0.11   10 ( 50)   27 ( 27) 
C  2569  3475 ch010109f1    766 (  0)  0.92 0.11 0.00    7 (  7)   30 ( 30) 
C  2574  3495 ce120109f1    802 (  0)  0.11 0.11 0.00    0 (  0)   33 ( 33) 
C  2924  3866 ff110109f1    795 (  0)  0.33 0.11 0.11    0 (  0)   41 ( 41) 
C  2996  3984 bd050109r1    782 (  0)  1.30 0.54 0.00    0 ( 46)   63 ( 63) 
C  3129  4084 ag100109r1    790 (  0)  0.45 0.00 0.00    8 (  8)   54 ( 54) 
C  3184  4144 fc030109r1    324 (  0)  0.51 1.03 0.00    0 (  0)  571 (571) 
C  3318  4291 cb050109r1    744 (  0)  1.47 0.68 0.00   89 (117)    0 (261) 

Overall discrep rates (%):             0.92 0.32 0.07

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90     796  18.6     796  18.6    0.00
 89      26   0.6     822  19.2    0.00
 88      18   0.4     840  19.6    0.00
 87      23   0.5     863  20.1    0.00
 86      17   0.4     880  20.5    0.00
 85      31   0.7     911  21.2    0.00
 84      20   0.5     931  21.7    0.00
 83      28   0.7     959  22.3    0.00
 82      23   0.5     982  22.9    0.00
 81      62   1.4    1044  24.3    0.00
 80      27   0.6    1071  25.0    0.00
 79      14   0.3    1085  25.3    0.00
 78       9   0.2    1094  25.5    0.00
 77      18   0.4    1112  25.9    0.00
 76      34   0.8    1146  26.7    0.00
 75      29   0.7    1175  27.4    0.00
 74      11   0.3    1186  27.6    0.00
 73      11   0.3    1197  27.9    0.00
 72      10   0.2    1207  28.1    0.00
 71      16   0.4    1223  28.5    0.00
 70       9   0.2    1232  28.7    0.00
 69       3   0.1    1235  28.8    0.00
 68      11   0.3    1246  29.0    0.00
 67       9   0.2    1255  29.2    0.00
 66     824  19.2    2079  48.5    0.00
 65       7   0.2    2086  48.6    0.00
 64       4   0.1    2090  48.7    0.00
 63       2   0.0    2092  48.8    0.00
 61     457  10.7    2549  59.4    0.00
 60     180   4.2    2729  63.6    0.00
 59       4   0.1    2733  63.7    0.00
 58      17   0.4    2750  64.1    0.00
 57       9   0.2    2759  64.3    0.00
 56     187   4.4    2946  68.7    0.00
 55      71   1.7    3017  70.3    0.00
 54      66   1.5    3083  71.8    0.00
 53     170   4.0    3253  75.8    0.00
 52     250   5.8    3503  81.6    0.00
 51     141   3.3    3644  84.9    0.01
 50      69   1.6    3713  86.5    0.01
 49      13   0.3    3726  86.8    0.01
 48      45   1.0    3771  87.9    0.01
 47      16   0.4    3787  88.3    0.01
 46      14   0.3    3801  88.6    0.01
 45      48   1.1    3849  89.7    0.01
 44      15   0.3    3864  90.0    0.01
 43      63   1.5    3927  91.5    0.01
 42      35   0.8    3962  92.3    0.02
 41       2   0.0    3964  92.4    0.02
 40      41   1.0    4005  93.3    0.02
 39       5   0.1    4010  93.5    0.02
 38       9   0.2    4019  93.7    0.02
 37      34   0.8    4053  94.5    0.03
 36       2   0.0    4055  94.5    0.03
 35      32   0.7    4087  95.2    0.04
 33       4   0.1    4091  95.3    0.04
 32       7   0.2    4098  95.5    0.05
 31       1   0.0    4099  95.5    0.05
 30       1   0.0    4100  95.5    0.05
 29       1   0.0    4101  95.6    0.05
 28       2   0.0    4103  95.6    0.05
 24       2   0.0    4105  95.7    0.06
 21       1   0.0    4106  95.7    0.07
 19       1   0.0    4107  95.7    0.08
 14       2   0.0    4109  95.8    0.16
 11       3   0.1    4112  95.8    0.40
 -1     179   4.2    4291 100.0  179.40   (quality -1 = terminal quality 0)

Avg. full length: 4291.0, trimmed (qual > -1): 4112.0
Avg. quality: 63.2 per base

Initial, terminal qual 0 segments:  1-80, 4193-4291

Regions of LLR- adjusted quality < 2.0:
1-80, 4159-4164, 4193-4291, 

3 regions, avg size 61.7, avg spacing 1430.3

First_start: 397, last_end: 4030

Slack, # used pairs (max_score), unused
 0    37  (19.3)     0 ( 0.0)       68
 1    28  (19.3)     0 ( 0.0)        6
 2     6  (18.5)     0 ( 0.0)        0
 4     3  (11.3)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 3008 - right     1284+      ag100109f1   (2048)    No           2243+

Bottom strand: 
 left -  1539     1539+      fh050109r1   (2489)    No           2489+
 4292 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56   1890   1890  17462 (100.00)   110  0    0   0   0   0     0 (0.00)    0  231 (1.32)
51   1239   3129  15572 ( 89.18)    39  0    0   0   0   0     0 (0.00)    0  231 (1.48)
50    750   3879  14333 ( 82.08)    40  0    0   0   0   0     0 (0.00)    0  231 (1.61)
48     81   3960  13583 ( 77.79)     0  0    0   0   0   0     0 (0.00)    0  231 (1.70)
47     71   4031  13502 ( 77.32)     1  0    0   0   0   0     0 (0.00)    0  231 (1.71)
46    306   4337  13431 ( 76.92)    18  0    0   0   0   0     0 (0.00)    0  231 (1.72)
45    380   4717  13125 ( 75.16)    18  0    0   0   0   0     0 (0.00)    0  231 (1.76)
44    538   5255  12745 ( 72.99)    17  0    0   0   0   0     0 (0.00)    0  231 (1.81)
43    676   5931  12207 ( 69.91)    57  0    0   0   0   0     0 (0.00)    0  231 (1.89)
42   1688   7619  11531 ( 66.03)    72  0    0   0   0   0     0 (0.00)    0  231 (2.00)
41    334   7953   9843 ( 56.37)    30  0    0   0   0   0     0 (0.00)    0  231 (2.35)
40    862   8815   9509 ( 54.46)    39  0    0   0   0   0     0 (0.00)    0  231 (2.43)
39    108   8923   8647 ( 49.52)     2  0    0   0   0   0     0 (0.00)    0  231 (2.67)
38    202   9125   8539 ( 48.90)     7  0    0   0   0   0     0 (0.00)    0  231 (2.71)
37    596   9721   8337 ( 47.74)    24  0    0   0   0   0     0 (0.00)    0  231 (2.77)
36     62   9783   7741 ( 44.33)     2  0    0   0   0   0     0 (0.00)    0  231 (2.98)
35    722  10505   7679 ( 43.98)    21  0    0   0   0   0     0 (0.00)    0  231 (3.01)
34    115  10620   6957 ( 39.84)     8  0    0   0   0   0     0 (0.00)    0  231 (3.32)
33    350  10970   6842 ( 39.18)     6  0    0   0   0   0     0 (0.00)    0  231 (3.38)
32    211  11181   6492 ( 37.18)     7  0    0   0   0   0     0 (0.00)    0  231 (3.56)
31     99  11280   6281 ( 35.97)     2  0    0   0   0   0     0 (0.00)    0  231 (3.68)
30    130  11410   6182 ( 35.40)     1  0    0   0   0   0     0 (0.00)    0  231 (3.74)
29    390  11800   6052 ( 34.66)     8  0    0   0   0   0     0 (0.00)    0  231 (3.82)
28    136  11936   5662 ( 32.42)     4  0    0   0   0   0     0 (0.00)    0  231 (4.08)
27    182  12118   5526 ( 31.65)     5  0    0   0   0   0     0 (0.00)    0  231 (4.18)
26     96  12214   5344 ( 30.60)     6  0    0   0   0   0     0 (0.00)    0  231 (4.32)
25    207  12421   5248 ( 30.05)     4  0    0   0   0   0     0 (0.00)    0  231 (4.40)
24    177  12598   5041 ( 28.87)     3  0    0   0   0   0     0 (0.00)    0  231 (4.58)
23    140  12738   4864 ( 27.85)     4  0    0   0   0   0     0 (0.00)    0  231 (4.75)
22    132  12870   4724 ( 27.05)     8  0    0   0   0   0     0 (0.00)    0  231 (4.89)
21    218  13088   4592 ( 26.30)     9  0    0   0   0   0     0 (0.00)    0  231 (5.03)
20    152  13240   4374 ( 25.05)     5  0    0   0   0   0     0 (0.00)    0  231 (5.28)
19    234  13474   4222 ( 24.18)    15  0    0   1   0   0     1 (0.43)    1  231 (5.47)
18    201  13675   3988 ( 22.84)     2  0    0   0   0   0     0 (0.00)    1  230 (5.77)
17    170  13845   3787 ( 21.69)     3  0    0   0   1   0     1 (0.59)    2  230 (6.07)
16    169  14014   3617 ( 20.71)    12  0    0   4   1   0     5 (2.96)    7  229 (6.33)
15    275  14289   3448 ( 19.75)     6  0    0   1   1   0     2 (0.73)    9  224 (6.50)
14    206  14495   3173 ( 18.17)     7  0    0   2   0   0     2 (0.97)   11  222 (7.00)
13    275  14770   2967 ( 16.99)    11  0    0   3   2   0     5 (1.82)   16  220 (7.41)
12    278  15048   2692 ( 15.42)     3  0    0   8   3   1    12 (4.32)   28  215 (7.99)
11    393  15441   2414 ( 13.82)     5  0    0  10   3   2    15 (3.82)   43  203 (8.41)
10    489  15930   2021 ( 11.57)     4  0    0  24   9   0    33 (6.75)   76  188 (9.30)
 9    622  16552   1532 (  8.77)     8  0    0  32   8   2    42 (6.75)  118  155 (10.12)
 8    419  16971    910 (  5.21)     7  0    0  28   7   6    41 (9.79)  159  113 (12.42)
 7    371  17342    491 (  2.81)     3  0    0  39  10   2    51 (13.75)  210   72 (14.66)
 6    115  17457    120 (  0.69)     0  0    0  10  11   0    21 (18.26)  231   21 (17.50)
 4      5  17462      5 (  0.03)     0  0    0   0   0   0     0 (0.00)  231    0 (0.00)
-1    123  17585      0 (  0.00)   734  0    0   0   0   0     0 (0.00)  231    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90   4186   4186  17219 (100.00)     0  0    0   0   0   0     0 (0.00)    0  194 (1.13)
89    132   4318  13033 ( 75.69)     0  0    0   0   0   0     0 (0.00)    0  194 (1.49)
88     87   4405  12901 ( 74.92)     0  0    0   0   0   0     0 (0.00)    0  194 (1.50)
87    118   4523  12814 ( 74.42)     0  0    0   0   0   0     0 (0.00)    0  194 (1.51)
86     77   4600  12696 ( 73.73)     0  0    0   0   0   0     0 (0.00)    0  194 (1.53)
85    130   4730  12619 ( 73.29)     0  0    0   0   0   0     0 (0.00)    0  194 (1.54)
84     96   4826  12489 ( 72.53)     0  0    0   0   0   0     0 (0.00)    0  194 (1.55)
83    124   4950  12393 ( 71.97)     0  0    0   0   0   0     0 (0.00)    0  194 (1.57)
82    108   5058  12269 ( 71.25)     0  0    0   0   0   0     0 (0.00)    0  194 (1.58)
81    240   5298  12161 ( 70.63)     0  0    0   0   0   0     0 (0.00)    0  194 (1.60)
80    121   5419  11921 ( 69.23)     0  0    0   0   0   0     0 (0.00)    0  194 (1.63)
79     41   5460  11800 ( 68.53)     0  0    0   0   0   0     0 (0.00)    0  194 (1.64)
78     32   5492  11759 ( 68.29)     0  0    0   0   0   0     0 (0.00)    0  194 (1.65)
77     89   5581  11727 ( 68.11)     0  0    0   0   0   0     0 (0.00)    0  194 (1.65)
76    152   5733  11638 ( 67.59)     0  0    0   0   0   0     0 (0.00)    0  194 (1.67)
75    104   5837  11486 ( 66.71)     0  0    0   0   0   0     0 (0.00)    0  194 (1.69)
74     38   5875  11382 ( 66.10)     0  0    0   0   0   0     0 (0.00)    0  194 (1.70)
73     40   5915  11344 ( 65.88)     0  0    0   0   0   0     0 (0.00)    0  194 (1.71)
72     32   5947  11304 ( 65.65)     0  0    0   0   0   0     0 (0.00)    0  194 (1.72)
71     51   5998  11272 ( 65.46)     0  0    0   0   0   0     0 (0.00)    0  194 (1.72)
70     30   6028  11221 ( 65.17)     0  0    0   0   0   0     0 (0.00)    0  194 (1.73)
69      9   6037  11191 ( 64.99)     0  0    0   0   0   0     0 (0.00)    0  194 (1.73)
68     51   6088  11182 ( 64.94)     0  0    0   0   0   0     0 (0.00)    0  194 (1.73)
67     40   6128  11131 ( 64.64)     0  0    0   0   0   0     0 (0.00)    0  194 (1.74)
66   3020   9148  11091 ( 64.41)     0  0    0   0   0   0     0 (0.00)    0  194 (1.75)
65     16   9164   8071 ( 46.87)     0  0    0   0   0   0     0 (0.00)    0  194 (2.40)
64     20   9184   8055 ( 46.78)     0  0    0   0   0   0     0 (0.00)    0  194 (2.41)
63      4   9188   8035 ( 46.66)     0  0    0   0   0   0     0 (0.00)    0  194 (2.41)
62     10   9198   8031 ( 46.64)     0  0    0   0   0   0     0 (0.00)    0  194 (2.42)
61   1629  10827   8021 ( 46.58)     0  0    0   0   0   0     0 (0.00)    0  194 (2.42)
60    709  11536   6392 ( 37.12)     0  0    0   0   0   0     0 (0.00)    0  194 (3.04)
59      9  11545   5683 ( 33.00)     0  0    0   0   0   0     0 (0.00)    0  194 (3.41)
58     44  11589   5674 ( 32.95)     0  0    0   0   0   0     0 (0.00)    0  194 (3.42)
57     45  11634   5630 ( 32.70)     0  0    0   0   0   0     0 (0.00)    0  194 (3.45)
56    411  12045   5585 ( 32.44)   110  0    0   0   0   0     0 (0.00)    0  194 (3.47)
55    291  12336   5174 ( 30.05)     0  0    0   0   0   0     0 (0.00)    0  194 (3.75)
54    258  12594   4883 ( 28.36)     0  0    0   0   0   0     0 (0.00)    0  194 (3.97)
53    561  13155   4625 ( 26.86)     0  0    0   0   0   0     0 (0.00)    0  194 (4.19)
52    937  14092   4064 ( 23.60)     0  0    0   0   0   0     0 (0.00)    0  194 (4.77)
51    294  14386   3127 ( 18.16)    39  0    0   0   0   0     0 (0.00)    0  194 (6.20)
50    177  14563   2833 ( 16.45)    40  0    0   0   0   0     0 (0.00)    0  194 (6.85)
49     51  14614   2656 ( 15.42)     0  0    0   0   0   0     0 (0.00)    0  194 (7.30)
48    151  14765   2605 ( 15.13)     0  0    0   0   0   0     0 (0.00)    0  194 (7.45)
47     54  14819   2454 ( 14.25)     1  0    0   0   0   0     0 (0.00)    0  194 (7.91)
46     39  14858   2400 ( 13.94)    18  0    0   0   0   0     0 (0.00)    0  194 (8.08)
45    123  14981   2361 ( 13.71)    18  0    0   0   0   0     0 (0.00)    0  194 (8.22)
44     38  15019   2238 ( 13.00)    17  0    0   0   0   0     0 (0.00)    0  194 (8.67)
43     78  15097   2200 ( 12.78)    57  0    0   0   0   0     0 (0.00)    0  194 (8.82)
42     74  15171   2122 ( 12.32)    68  0    0   0   0   0     0 (0.00)    0  194 (9.14)
41     23  15194   2048 ( 11.89)    30  0    0   0   0   0     0 (0.00)    0  194 (9.47)
40    371  15565   2025 ( 11.76)    39  0    0   0   0   0     0 (0.00)    0  194 (9.58)
39     22  15587   1654 (  9.61)     0  0    0   0   0   0     0 (0.00)    0  194 (11.73)
38     15  15602   1632 (  9.48)     7  0    0   0   0   0     0 (0.00)    0  194 (11.89)
37     46  15648   1617 (  9.39)    24  0    0   0   0   0     0 (0.00)    0  194 (12.00)
36     25  15673   1571 (  9.12)     2  0    0   0   0   0     0 (0.00)    0  194 (12.35)
35     49  15722   1546 (  8.98)    15  0    0   0   0   0     0 (0.00)    0  194 (12.55)
34     23  15745   1497 (  8.69)     1  0    0   0   0   0     0 (0.00)    0  194 (12.96)
33     18  15763   1474 (  8.56)     0  0    0   0   0   0     0 (0.00)    0  194 (13.16)
32     23  15786   1456 (  8.46)     3  0    0   0   0   0     0 (0.00)    0  194 (13.32)
31      7  15793   1433 (  8.32)     0  0    0   0   0   0     0 (0.00)    0  194 (13.54)
30     11  15804   1426 (  8.28)     0  0    0   0   0   0     0 (0.00)    0  194 (13.60)
29     19  15823   1415 (  8.22)     0  0    0   0   0   0     0 (0.00)    0  194 (13.71)
28     12  15835   1396 (  8.11)     2  0    0   0   0   0     0 (0.00)    0  194 (13.90)
27     13  15848   1384 (  8.04)     0  0    0   0   0   0     0 (0.00)    0  194 (14.02)
26     16  15864   1371 (  7.96)     0  0    0   0   0   0     0 (0.00)    0  194 (14.15)
25    219  16083   1355 (  7.87)     0  0    0   0   0   0     0 (0.00)    0  194 (14.32)
24     16  16099   1136 (  6.60)     0  0    0   0   0   0     0 (0.00)    0  194 (17.08)
23     16  16115   1120 (  6.50)     0  0    0   0   0   0     0 (0.00)    0  194 (17.32)
22      4  16119   1104 (  6.41)     0  0    0   0   0   0     0 (0.00)    0  194 (17.57)
21     13  16132   1100 (  6.39)     0  0    0   0   0   0     0 (0.00)    0  194 (17.64)
20     11  16143   1087 (  6.31)     0  0    0   0   0   0     0 (0.00)    0  194 (17.85)
19     26  16169   1076 (  6.25)     0  0    0   1   0   0     1 (3.85)    1  194 (18.03)
18      9  16178   1050 (  6.10)     0  0    0   0   0   0     0 (0.00)    1  193 (18.38)
17     16  16194   1041 (  6.05)     0  0    0   0   1   0     1 (6.25)    2  193 (18.54)
16     36  16230   1025 (  5.95)     0  0    0   3   0   0     3 (8.33)    5  192 (18.73)
15     38  16268    989 (  5.74)     0  0    0   0   1   0     1 (2.63)    6  189 (19.11)
14     30  16298    951 (  5.52)     0  0    0   2   0   0     2 (6.67)    8  188 (19.77)
13     62  16360    921 (  5.35)     0  0    0   3   2   0     5 (8.06)   13  186 (20.20)
12     50  16410    859 (  4.99)     0  0    0   7   3   1    11 (22.00)   24  181 (21.07)
11    109  16519    809 (  4.70)     0  0    0   7   3   2    12 (11.01)   36  170 (21.01)
10    129  16648    700 (  4.07)     0  0    0  19   6   0    25 (19.38)   61  158 (22.57)
 9    192  16840    571 (  3.32)     0  0    0  26   8   2    36 (18.75)   97  133 (23.29)
 8    154  16994    379 (  2.20)     0  0    0  23   7   5    35 (22.73)  132   97 (25.59)
 7    164  17158    225 (  1.31)     0  0    0  35   7   1    43 (26.22)  175   62 (27.56)
 6     60  17218     61 (  0.35)     0  0    0   9  10   0    19 (31.67)  194   19 (31.15)
 4      1  17219      1 (  0.01)     0  0    0   0   0   0     0 (0.00)  194    0 (0.00)
-1    366  17585      0 (  0.00)   906  0    0  27   8   2    37 (10.11)  231    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     179      179        2
 11       3      182        3
 14       2      184        3
 19       1      185        3
 21       1      186        3
 24       2      188        3
 28       2      190        4
 29       1      191        4
 30       1      192        5
 31       1      193        6
 32       7      200        6
 33       4      204        7
 35      32      236       14
 36       2      238       15
 37      34      272       27
 38       9      281       31
 39       5      286       30
 40      41      327       25
 41       2      329       26
 42      35      364       31
 43      63      427       39
 44      15      442       45
 45      48      490       53
 46      14      504       51
 47      16      520       55
 48      45      565       66
 49      13      578       66
 50      69      647       67
 51     141      788       86
 52     250     1038      146
 53     170     1208      162
 54      66     1274      175
 55      71     1345      186
 56     187     1532      154
 57       9     1541      156
 58      17     1558      156
 59       4     1562      159
 60     180     1742      160
 61     457     2199      168
 63       2     2201      169
 64       4     2205      171
 65       7     2212      173
 66     824     3036       19
 67       9     3045       23
 68      11     3056       24
 69       3     3059       25
 70       9     3068       26
 71      16     3084       30
 72      10     3094       32
 73      11     3105       36
 74      11     3116       38
 75      29     3145       47
 76      34     3179       55
 77      18     3197       58
 78       9     3206       56
 79      14     3220       56
 80      27     3247       64
 81      62     3309       64
 82      23     3332       70
 83      28     3360       75
 84      20     3380       76
 85      31     3411       73
 86      17     3428       73
 87      23     3451       72
 88      18     3469       74
 89      26     3495       75
 90     796     4291        1

SS region: 2823 (65.79%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  3184- 3573 [-34.6] (491,0)   C fc030109r1         965-572 || local(+/-) (8.6,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -0.5 (<20 part: -0.5 (#=6), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.5), match: 8.6  trail: -42.8  total: -34.7 

Gaps in unique-read coverage:  None.

Contig 8.  30 reads; 3302 bp (untrimmed), 3174 (trimmed).
      1   966 fc060109r1    870 (  0)  0.41 0.21 0.10    0 (190)    0 (  4) 
    162  1126 cc090109f1    824 (  0)  0.64 0.11 0.00   29 ( 29)    0 (  0) 
    458  1391 bg080109f1    805 (  0)  0.22 0.33 0.00   28 ( 28)    0 (  0) 
    854  1821 bd070109r1    799 (  0)  0.44 0.11 0.22   50 ( 50)    0 (  0) 
    878  1856 df060109r1    830 (  0)  0.00 0.11 0.00   46 ( 46)    5 (  5) 
    896  1829 ea090109f1    791 (  0)  0.55 0.22 0.00   31 ( 31)    0 (  0) 
   1091  2051 ch050109f1    821 (  0)  0.32 0.21 0.11   29 ( 29)    0 (  0) 
   1156  2117 fc090109r1    819 (  0)  0.11 0.00 0.11   52 ( 52)    1 (  1) 
   1342  2291 ae020109f1    830 (  0)  0.00 0.00 0.00   31 ( 31)    0 (  0) 
   1416  2335 ec110109f1    790 (  0)  0.34 0.11 0.11   30 ( 30)    0 (  0) 
   1426  2404 ac100109r1    810 (  0)  0.44 0.11 0.11   70 ( 70)    1 (  1) 
   1493  2433 cc110109r1    796 (  0)  0.56 0.00 0.11   52 ( 52)    2 (  2) 
   1600  2566 dd090109r1    774 (  0)  1.65 1.10 0.00   50 ( 50)    6 ( 82) 
C  1699  2671 fc060109f1    864 ( 98)  0.32 0.21 0.21    0 ( 16)   37 ( 36) 
   1742  2693 ee030109f1    849 (162)  0.87 0.22 0.11   27 ( 27)    1 ( 30) 
C  1774  2714 bg080109r1    817 (142)  0.11 0.34 0.45    2 (  0)   49 ( 49) 
   1797  2745 de110109r1    706 (172)  3.78 1.03 0.11   62 ( 88)   13 ( 86) 
C  1836  2875 cc090109r1    335 (315)  3.76 1.17 0.94  577 (667)   37 ( 52) 
   1873  2839 dg080109r1    831 (268)  1.31 0.00 0.54   46 ( 46)    3 ( 16) 
   1892  2829 ec100109f1    857 (314)  0.55 0.22 0.00   31 ( 54)    1 (  1) 
   1908  2850 ba070109r1    861 (334)  0.34 0.00 0.00   49 ( 49)    0 (  0) 
   2030  2968 eb060109r1    751 (338)  3.27 0.79 0.00   48 ( 48)    4 (127) 
   2049  2977 fb120109r1    857 (435)  0.23 0.00 0.00   51 ( 51)    1 (  1) 
   2057  3004 da100109r1    862 (443)  0.67 0.00 0.11   50 ( 50)    0 (  0) 
   2057  3001 ca010109f1    847 (421)  1.31 0.00 0.33   30 ( 30)    2 ( 19) 
   2173  3108 ad120109r1    863 (585)  0.23 0.00 0.00   53 ( 53)    5 (  5) 
   2178  3123 dc010109r1    366 (127)  8.45 2.20 0.51   35 ( 55)  319 (483) 
   2186  3114 be100109f1    872 (583)  0.44 0.11 0.11   24 ( 24)    3 (  3) 
C  2292  3240 ea090109r1    885 (677)  0.22 0.00 0.00    0 (  0)   49 ( 49) 
   2391  3302 bh110109f1    868 (755)  0.00 0.00 0.00   29 ( 29)    0 (111) 

Overall discrep rates (%):             0.91 0.26 0.12

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    1181  35.8    1181  35.8    0.00
 89       5   0.2    1186  35.9    0.00
 88      15   0.5    1201  36.4    0.00
 87       4   0.1    1205  36.5    0.00
 86      12   0.4    1217  36.9    0.00
 85      19   0.6    1236  37.4    0.00
 84       6   0.2    1242  37.6    0.00
 83      12   0.4    1254  38.0    0.00
 82      14   0.4    1268  38.4    0.00
 81      31   0.9    1299  39.3    0.00
 80      14   0.4    1313  39.8    0.00
 79       6   0.2    1319  39.9    0.00
 78       9   0.3    1328  40.2    0.00
 77       7   0.2    1335  40.4    0.00
 76      15   0.5    1350  40.9    0.00
 75      15   0.5    1365  41.3    0.00
 74      11   0.3    1376  41.7    0.00
 73       4   0.1    1380  41.8    0.00
 72       7   0.2    1387  42.0    0.00
 71       3   0.1    1390  42.1    0.00
 70       5   0.2    1395  42.2    0.00
 69       5   0.2    1400  42.4    0.00
 68      10   0.3    1410  42.7    0.00
 67       3   0.1    1413  42.8    0.00
 66     641  19.4    2054  62.2    0.00
 65       2   0.1    2056  62.3    0.00
 64       9   0.3    2065  62.5    0.00
 63       1   0.0    2066  62.6    0.00
 62       6   0.2    2072  62.7    0.00
 61     449  13.6    2521  76.3    0.00
 60      39   1.2    2560  77.5    0.00
 59       1   0.0    2561  77.6    0.00
 57       2   0.1    2563  77.6    0.00
 56      48   1.5    2611  79.1    0.00
 55      96   2.9    2707  82.0    0.00
 54      22   0.7    2729  82.6    0.00
 53     174   5.3    2903  87.9    0.00
 52      35   1.1    2938  89.0    0.00
 51      60   1.8    2998  90.8    0.00
 50      14   0.4    3012  91.2    0.00
 48       5   0.2    3017  91.4    0.00
 46       6   0.2    3023  91.6    0.00
 45      25   0.8    3048  92.3    0.00
 44       1   0.0    3049  92.3    0.00
 43       1   0.0    3050  92.4    0.00
 42      17   0.5    3067  92.9    0.00
 40      18   0.5    3085  93.4    0.01
 37       9   0.3    3094  93.7    0.01
 36       1   0.0    3095  93.7    0.01
 35      25   0.8    3120  94.5    0.02
 34       2   0.1    3122  94.5    0.02
 33      10   0.3    3132  94.9    0.02
 31       1   0.0    3133  94.9    0.02
 30       4   0.1    3137  95.0    0.03
 29       2   0.1    3139  95.1    0.03
 28       1   0.0    3140  95.1    0.03
 27       3   0.1    3143  95.2    0.04
 26       1   0.0    3144  95.2    0.04
 25       3   0.1    3147  95.3    0.05
 24       5   0.2    3152  95.5    0.07
 23       2   0.1    3154  95.5    0.08
 21       1   0.0    3155  95.5    0.09
 20       3   0.1    3158  95.6    0.12
 19       2   0.1    3160  95.7    0.14
 18       5   0.2    3165  95.9    0.22
 17       1   0.0    3166  95.9    0.24
 16       1   0.0    3167  95.9    0.27
 15       3   0.1    3170  96.0    0.36
 14       2   0.1    3172  96.1    0.44
 13       2   0.1    3174  96.1    0.54
 -1     128   3.9    3302 100.0  128.54   (quality -1 = terminal quality 0)

Avg. full length: 3302.0, trimmed (qual > -1): 3174.0
Avg. quality: 69.0 per base

Initial, terminal qual 0 segments:  1-80, 3255-3302

Regions of LLR- adjusted quality < 2.0:
1-80, 3192-3194, 3213-3216, 3238-3240, 3242, 3245-3246, 3249, 3253-3302, 


8 regions, avg size 18.0, avg spacing 412.8

First_start: 191, last_end: 3191

Slack, # used pairs (max_score), unused
 0   128  (19.3)     0 ( 0.0)      272
 1   109  (19.8)     0 ( 0.0)       14
 2    32  (19.1)     0 ( 0.0)        0
 3    17  (17.1)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 3303 - right        0+      bh110109f1   (2391)    No            911+

Bottom strand: 
 left -  1698     1698+      fc060109f1   (2671)    No           2671+
 3192 - right      111+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56   3887   3887  26390 (100.00)     0  0    0   0   0   0     0 (0.00)    0  341 (1.29)
51   2604   6491  22503 ( 85.27)     0  0    0   0   0   0     0 (0.00)    0  341 (1.52)
50    516   7007  19899 ( 75.40)     0  0    0   0   0   0     0 (0.00)    0  341 (1.71)
48     89   7096  19383 ( 73.45)     0  0    0   0   0   0     0 (0.00)    0  341 (1.76)
47     68   7164  19294 ( 73.11)     0  0    0   0   0   0     0 (0.00)    0  341 (1.77)
46    509   7673  19226 ( 72.85)     0  0    0   0   0   0     0 (0.00)    0  341 (1.77)
45    894   8567  18717 ( 70.92)     0  0    0   0   0   0     0 (0.00)    0  341 (1.82)
44    446   9013  17823 ( 67.54)     0  0    0   0   0   0     0 (0.00)    0  341 (1.91)
43   1701  10714  17377 ( 65.85)     0  0    0   0   0   0     0 (0.00)    0  341 (1.96)
42   1760  12474  15676 ( 59.40)     1  0    0   0   0   0     0 (0.00)    0  341 (2.18)
41    516  12990  13916 ( 52.73)     0  0    0   0   0   0     0 (0.00)    0  341 (2.45)
40   1830  14820  13400 ( 50.78)     0  0    0   0   0   0     0 (0.00)    0  341 (2.54)
39    128  14948  11570 ( 43.84)     0  0    0   0   0   0     0 (0.00)    0  341 (2.95)
38    225  15173  11442 ( 43.36)     0  0    0   0   0   0     0 (0.00)    0  341 (2.98)
37    642  15815  11217 ( 42.50)     1  0    0   0   0   0     0 (0.00)    0  341 (3.04)
36     60  15875  10575 ( 40.07)     0  0    0   0   0   0     0 (0.00)    0  341 (3.22)
35    936  16811  10515 ( 39.84)     1  0    0   0   0   0     0 (0.00)    0  341 (3.24)
34    218  17029   9579 ( 36.30)     3  0    0   0   0   0     0 (0.00)    0  341 (3.56)
33    347  17376   9361 ( 35.47)     0  0    0   0   0   0     0 (0.00)    0  341 (3.64)
32    346  17722   9014 ( 34.16)     1  0    0   0   0   0     0 (0.00)    0  341 (3.78)
31    151  17873   8668 ( 32.85)     1  0    0   0   0   0     0 (0.00)    0  341 (3.93)
30    180  18053   8517 ( 32.27)     1  0    0   0   0   0     0 (0.00)    0  341 (4.00)
29    607  18660   8337 ( 31.59)    17  0    0   0   0   0     0 (0.00)    0  341 (4.09)
28    206  18866   7730 ( 29.29)     2  0    0   0   0   0     0 (0.00)    0  341 (4.41)
27    305  19171   7524 ( 28.51)    12  0    0   1   0   0     1 (0.33)    1  341 (4.53)
26    135  19306   7219 ( 27.36)     5  0    0   0   0   0     0 (0.00)    1  340 (4.71)
25    332  19638   7084 ( 26.84)    10  0    0   0   0   0     0 (0.00)    1  340 (4.80)
24    312  19950   6752 ( 25.59)    13  0    0   0   0   0     0 (0.00)    1  340 (5.04)
23    226  20176   6440 ( 24.40)     5  0    0   1   0   0     1 (0.44)    2  340 (5.28)
22    218  20394   6214 ( 23.55)    16  0    0   0   0   0     0 (0.00)    2  339 (5.46)
21    305  20699   5996 ( 22.72)     2  0    0   1   1   0     2 (0.66)    4  339 (5.65)
20    217  20916   5691 ( 21.56)     9  0    0   0   0   0     0 (0.00)    4  337 (5.92)
19    371  21287   5474 ( 20.74)    21  0    0   0   1   0     1 (0.27)    5  337 (6.16)
18    265  21552   5103 ( 19.34)     8  0    0   0   1   0     1 (0.38)    6  336 (6.58)
17    224  21776   4838 ( 18.33)     8  0    0   0   0   1     1 (0.45)    7  335 (6.92)
16    270  22046   4614 ( 17.48)    26  0    0   5   0   0     5 (1.85)   12  334 (7.24)
15    371  22417   4344 ( 16.46)     4  0    0   4   2   1     7 (1.89)   19  329 (7.57)
14    258  22675   3973 ( 15.05)     9  0    0   5   2   1     8 (3.10)   27  322 (8.10)
13    394  23069   3715 ( 14.08)    12  0    0   9   1   0    10 (2.54)   37  314 (8.45)
12    408  23477   3321 ( 12.58)     3  0    0   7   6   0    13 (3.19)   50  304 (9.15)
11    431  23908   2913 ( 11.04)     5  0    0  18   4   2    24 (5.57)   74  291 (9.99)
10    565  24473   2482 (  9.41)    15  0    0  24   5   5    34 (6.02)  108  267 (10.76)
 9    790  25263   1917 (  7.26)    31  0    0  51  10  15    76 (9.62)  184  233 (12.15)
 8    538  25801   1127 (  4.27)    12  0    0  47   9   1    57 (10.59)  241  157 (13.93)
 7    379  26180    589 (  2.23)    14  0    0  43   6   4    53 (13.98)  294  100 (16.98)
 6    178  26358    210 (  0.80)    14  0    0  19  16   3    38 (21.35)  332   47 (22.38)
 4     28  26386     32 (  0.12)     3  0    0   3   2   0     5 (17.86)  337    9 (28.12)
 0      4  26390      4 (  0.02)     0  0    2   0   2   0     4 (100.00)  341    4 (100.00)
-1     56  26446      0 (  0.00)  1866  0    0   0   0   0     0 (0.00)  341    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  14396  14396  25630 (100.00)     0  0    0   0   0   0     0 (0.00)    0  188 (0.73)
89     36  14432  11234 ( 43.83)     0  0    0   0   0   0     0 (0.00)    0  188 (1.67)
88    149  14581  11198 ( 43.69)     0  0    0   0   0   0     0 (0.00)    0  188 (1.68)
87     32  14613  11049 ( 43.11)     0  0    0   0   0   0     0 (0.00)    0  188 (1.70)
86     58  14671  11017 ( 42.98)     0  0    0   0   0   0     0 (0.00)    0  188 (1.71)
85     86  14757  10959 ( 42.76)     0  0    0   0   0   0     0 (0.00)    0  188 (1.72)
84     54  14811  10873 ( 42.42)     0  0    0   0   0   0     0 (0.00)    0  188 (1.73)
83     93  14904  10819 ( 42.21)     0  0    0   0   0   0     0 (0.00)    0  188 (1.74)
82     79  14983  10726 ( 41.85)     0  0    0   0   0   0     0 (0.00)    0  188 (1.75)
81    281  15264  10647 ( 41.54)     0  0    0   0   0   0     0 (0.00)    0  188 (1.77)
80     35  15299  10366 ( 40.44)     0  0    0   0   0   0     0 (0.00)    0  188 (1.81)
79     16  15315  10331 ( 40.31)     0  0    0   0   0   0     0 (0.00)    0  188 (1.82)
78     35  15350  10315 ( 40.25)     0  0    0   0   0   0     0 (0.00)    0  188 (1.82)
77     11  15361  10280 ( 40.11)     0  0    0   0   0   0     0 (0.00)    0  188 (1.83)
76     65  15426  10269 ( 40.07)     0  0    0   0   0   0     0 (0.00)    0  188 (1.83)
75     31  15457  10204 ( 39.81)     0  0    0   0   0   0     0 (0.00)    0  188 (1.84)
74     19  15476  10173 ( 39.69)     0  0    0   0   0   0     0 (0.00)    0  188 (1.85)
73      8  15484  10154 ( 39.62)     0  0    0   0   0   0     0 (0.00)    0  188 (1.85)
72     13  15497  10146 ( 39.59)     0  0    0   0   0   0     0 (0.00)    0  188 (1.85)
71      9  15506  10133 ( 39.54)     0  0    0   0   0   0     0 (0.00)    0  188 (1.86)
70     21  15527  10124 ( 39.50)     0  0    0   0   0   0     0 (0.00)    0  188 (1.86)
69     12  15539  10103 ( 39.42)     0  0    0   0   0   0     0 (0.00)    0  188 (1.86)
68     16  15555  10091 ( 39.37)     0  0    0   0   0   0     0 (0.00)    0  188 (1.86)
67     17  15572  10075 ( 39.31)     0  0    0   0   0   0     0 (0.00)    0  188 (1.87)
66   3598  19170  10058 ( 39.24)     0  0    0   0   0   0     0 (0.00)    0  188 (1.87)
65     15  19185   6460 ( 25.20)     0  0    0   0   0   0     0 (0.00)    0  188 (2.91)
64     18  19203   6445 ( 25.15)     0  0    0   0   0   0     0 (0.00)    0  188 (2.92)
63      2  19205   6427 ( 25.08)     0  0    0   0   0   0     0 (0.00)    0  188 (2.93)
62     19  19224   6425 ( 25.07)     0  0    0   0   0   0     0 (0.00)    0  188 (2.93)
61   2299  21523   6406 ( 24.99)     0  0    0   0   0   0     0 (0.00)    0  188 (2.93)
60    120  21643   4107 ( 16.02)     0  0    0   0   0   0     0 (0.00)    0  188 (4.58)
59     12  21655   3987 ( 15.56)     0  0    0   0   0   0     0 (0.00)    0  188 (4.72)
58     17  21672   3975 ( 15.51)     0  0    0   0   0   0     0 (0.00)    0  188 (4.73)
57     15  21687   3958 ( 15.44)     0  0    0   0   0   0     0 (0.00)    0  188 (4.75)
56    195  21882   3943 ( 15.38)     0  0    0   0   0   0     0 (0.00)    0  188 (4.77)
55    406  22288   3748 ( 14.62)     0  0    0   0   0   0     0 (0.00)    0  188 (5.02)
54    104  22392   3342 ( 13.04)     0  0    0   0   0   0     0 (0.00)    0  188 (5.63)
53    703  23095   3238 ( 12.63)     0  0    0   0   0   0     0 (0.00)    0  188 (5.81)
52    118  23213   2535 (  9.89)     0  0    0   0   0   0     0 (0.00)    0  188 (7.42)
51    158  23371   2417 (  9.43)     0  0    0   0   0   0     0 (0.00)    0  188 (7.78)
50     67  23438   2259 (  8.81)     0  0    0   0   0   0     0 (0.00)    0  188 (8.32)
49     25  23463   2192 (  8.55)     0  0    0   0   0   0     0 (0.00)    0  188 (8.58)
48     30  23493   2167 (  8.45)     0  0    0   0   0   0     0 (0.00)    0  188 (8.68)
47     23  23516   2137 (  8.34)     0  0    0   0   0   0     0 (0.00)    0  188 (8.80)
46     29  23545   2114 (  8.25)     0  0    0   0   0   0     0 (0.00)    0  188 (8.89)
45     54  23599   2085 (  8.13)     0  0    0   0   0   0     0 (0.00)    0  188 (9.02)
44     48  23647   2031 (  7.92)     0  0    0   0   0   0     0 (0.00)    0  188 (9.26)
43     31  23678   1983 (  7.74)     0  0    0   0   0   0     0 (0.00)    0  188 (9.48)
42     48  23726   1952 (  7.62)     0  0    0   0   0   0     0 (0.00)    0  188 (9.63)
41     31  23757   1904 (  7.43)     0  0    0   0   0   0     0 (0.00)    0  188 (9.87)
40    427  24184   1873 (  7.31)     0  0    0   0   0   0     0 (0.00)    0  188 (10.04)
39     22  24206   1446 (  5.64)     0  0    0   0   0   0     0 (0.00)    0  188 (13.00)
38      6  24212   1424 (  5.56)     0  0    0   0   0   0     0 (0.00)    0  188 (13.20)
37     18  24230   1418 (  5.53)     0  0    0   0   0   0     0 (0.00)    0  188 (13.26)
36     11  24241   1400 (  5.46)     0  0    0   0   0   0     0 (0.00)    0  188 (13.43)
35     35  24276   1389 (  5.42)     0  0    0   0   0   0     0 (0.00)    0  188 (13.53)
34     18  24294   1354 (  5.28)     1  0    0   0   0   0     0 (0.00)    0  188 (13.88)
33     25  24319   1336 (  5.21)     0  0    0   0   0   0     0 (0.00)    0  188 (14.07)
32     14  24333   1311 (  5.12)     0  0    0   0   0   0     0 (0.00)    0  188 (14.34)
31     12  24345   1297 (  5.06)     0  0    0   0   0   0     0 (0.00)    0  188 (14.49)
30      7  24352   1285 (  5.01)     0  0    0   0   0   0     0 (0.00)    0  188 (14.63)
29     28  24380   1278 (  4.99)     0  0    0   0   0   0     0 (0.00)    0  188 (14.71)
28      7  24387   1250 (  4.88)     0  0    0   0   0   0     0 (0.00)    0  188 (15.04)
27     21  24408   1243 (  4.85)     2  0    0   1   0   1     2 (9.52)    2  188 (15.12)
26      9  24417   1222 (  4.77)     0  0    0   0   0   0     0 (0.00)    2  186 (15.22)
25    105  24522   1213 (  4.73)     0  0    0   0   0   0     0 (0.00)    2  186 (15.33)
24     19  24541   1108 (  4.32)     1  0    0   0   0   0     0 (0.00)    2  186 (16.79)
23     12  24553   1089 (  4.25)     0  0    0   1   0   0     1 (8.33)    3  186 (17.08)
22     11  24564   1077 (  4.20)     0  0    0   0   0   0     0 (0.00)    3  185 (17.18)
21     21  24585   1066 (  4.16)     0  0    0   1   0   0     1 (4.76)    4  185 (17.35)
20     21  24606   1045 (  4.08)     0  0    0   0   0   0     0 (0.00)    4  184 (17.61)
19     33  24639   1024 (  4.00)     1  0    0   0   1   0     1 (3.03)    5  184 (17.97)
18     18  24657    991 (  3.87)     0  0    0   0   1   0     1 (5.56)    6  183 (18.47)
17     21  24678    973 (  3.80)     0  0    0   0   0   1     1 (4.76)    7  182 (18.71)
16     35  24713    952 (  3.71)     0  0    0   4   0   0     4 (11.43)   11  181 (19.01)
15     44  24757    917 (  3.58)     0  0    0   3   2   1     6 (13.64)   17  177 (19.30)
14     26  24783    873 (  3.41)     0  0    0   3   1   0     4 (15.38)   21  171 (19.59)
13     70  24853    847 (  3.30)     0  0    0   5   1   0     6 (8.57)   27  167 (19.72)
12     54  24907    777 (  3.03)     0  0    0   2   4   0     6 (11.11)   33  161 (20.72)
11     70  24977    723 (  2.82)     0  0    0   9   2   1    12 (17.14)   45  155 (21.44)
10    103  25080    653 (  2.55)     0  0    0  10   1   4    15 (14.56)   60  143 (21.90)
 9    185  25265    550 (  2.15)     3  0    0  19   4  10    33 (17.84)   93  128 (23.27)
 8    152  25417    365 (  1.42)     0  0    0  30   6   1    37 (24.34)  130   95 (26.03)
 7    129  25546    213 (  0.83)     0  0    0  29   1   4    34 (26.36)  164   58 (27.23)
 6     60  25606     84 (  0.33)     0  0    0  11   6   0    17 (28.33)  181   24 (28.57)
 4     20  25626     24 (  0.09)     0  0    0   2   1   0     3 (15.00)  184    7 (29.17)
 0      4  25630      4 (  0.02)     0  0    2   0   2   0     4 (100.00)  188    4 (100.00)
-1    816  26446      0 (  0.00)  2143  0    0 108  35  10   153 (18.75)  341    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     128      128        2
 13       2      130        4
 14       2      132        6
 15       3      135        7
 16       1      136        6
 17       1      137        6
 18       5      142        6
 19       2      144        8
 20       3      147        8
 21       1      148        7
 23       2      150        7
 24       5      155        7
 25       3      158        7
 26       1      159        6
 27       3      162        5
 28       1      163        5
 29       2      165        5
 30       4      169        6
 31       1      170        7
 33      10      180        4
 34       2      182        6
 35      25      207        9
 36       1      208        9
 37       9      217        8
 40      18      235       11
 42      17      252       11
 43       1      253       11
 44       1      254       11
 45      25      279       11
 46       6      285       10
 48       5      290       13
 50      14      304       20
 51      60      364       32
 52      35      399       46
 53     174      573       82
 54      22      595       86
 55      96      691       91
 56      48      739       90
 57       2      741       90
 59       1      742       91
 60      39      781       95
 61     449     1230      116
 62       6     1236      119
 63       1     1237      120
 64       9     1246      120
 65       2     1248      120
 66     641     1889       11
 67       3     1892       13
 68      10     1902       14
 69       5     1907       15
 70       5     1912       16
 71       3     1915       18
 72       7     1922       19
 73       4     1926       22
 74      11     1937       25
 75      15     1952       23
 76      15     1967       22
 77       7     1974       23
 78       9     1983       24
 79       6     1989       24
 80      14     2003       24
 81      31     2034       29
 82      14     2048       30
 83      12     2060       33
 84       6     2066       32
 85      19     2085       32
 86      12     2097       30
 87       4     2101       30
 88      15     2116       33
 89       5     2121       32
 90    1181     3302        1

SS region: 1809 (54.78%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads): None.

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(5, 0)  2420- 3302 [15.4] (0,0)     bh110109f1         30-912 | 25 912 | DA:(**25 29**)(**802 912**) || local(+/-) (13.9,0.0), distant (14.0,0.0)

Gaps in unique-read coverage:   E 2485- 3191

Contig 9.  104 reads; 12333 bp (untrimmed), 12317 (trimmed).
     -1   939 ch100109f1    706 (  0)  2.56 0.00 0.35   55 ( 55)   28 ( 87) 
      1   955 ah090109r1    883 (  0)  0.21 0.00 0.10    0 ( 16)    0 (  0) 
      3   935 eh020109r1    845 (  0)  0.33 0.00 0.00   14 ( 14)    1 (  1) 
    463  1446 ad070109f1    805 (  0)  0.53 0.11 0.21   45 ( 45)    1 (  1) 
    465  1411 cd010109r1    676 (  0)  4.55 0.11 0.44   45 (163)    1 ( 22) 
C   864  1850 ad070109r1    815 (  0)  0.11 0.00 0.22    0 (  0)   68 ( 68) 
    886  1855 cg070109f1    835 (  0)  0.21 0.00 0.11   31 ( 31)    0 (  0) 
    932  1900 dd030109f1    784 (  0)  2.02 0.32 0.11   29 ( 85)    0 (  0) 
   1076  2020 ed070109f1    780 (  0)  0.77 0.22 0.00   31 ( 36)    0 (  0) 
   1166  2108 ac110109r1    778 (  0)  0.11 0.00 0.00   54 ( 54)    0 (  0) 
   1168  2118 cc100109r1    667 (  0)  2.25 0.35 0.12   47 ( 47)   58 (122) 
   1322  2369 dd020109r1    187 (  0)  14.61 0.62 1.03   83 (143)  479 (583) 
   1386  2348 bd030109r1    833 (  0)  0.11 0.00 0.11   49 ( 49)    0 (  0) 
C  1454  2396 ch100109r1    655 (  0)  3.92 1.68 0.11    0 (103)   51 ( 97) 
   1495  2454 aa060109r1    835 (  0)  0.44 0.00 0.00   54 ( 54)    0 (  0) 
C  1542  2464 eh020109f1    694 (  0)  3.47 1.34 0.22    0 (141)   30 ( 30) 
   1645  2574 be020109f1    800 (  0)  0.89 0.67 0.00   29 ( 29)    0 (  0) 
C  1813  2775 ah090109f1    859 (  0)  0.22 0.22 0.00    0 (  0)   35 ( 35) 
   1934  2856 fg110109f1    809 (  0)  1.01 0.22 0.11   27 ( 27)    6 ( 13) 
C  1978  2920 cd010109f1    753 (  0)  3.49 0.55 0.22    3 (  3)   24 ( 51) 
C  2082  3061 db050109r1    804 (  0)  2.37 0.32 0.32    3 ( 24)   47 ( 47) 
C  2312  3268 cc100109f1    873 (  0)  0.22 0.00 0.11    2 (  2)   30 ( 30) 
C  2393  3345 eb030109f1    874 (  0)  0.00 0.00 0.00    1 (  1)   30 ( 30) 
C  2517  3463 ac110109f1    865 (  0)  0.00 0.00 0.00    0 (  0)   33 ( 33) 
C  2540  3503 dd020109f1    854 (  0)  0.75 0.11 0.21    0 (  0)   28 ( 60) 
C  2564  3533 aa060109f1    826 (  0)  0.65 0.87 0.00   12 ( 17)   35 ( 35) 
C  2788  3804 cg070109r1    302 (  0)  6.49 0.48 0.24  542 (578)   59 ( 69) 
C  2835  3785 bd030109f1    869 (  0)  0.11 0.00 0.00    0 (  0)   32 ( 32) 
C  3375  4307 fg110109r1    779 (  0)  1.25 0.34 0.34    0 (  0)   55 (555) 
C  4119  5067 be020109r1    850 (  0)  0.33 0.00 0.11    0 (152)   49 ( 49) 
   4233  5163 ag010109f1    857 (  0)  0.22 0.11 0.00   34 ( 39)    0 (  0) 
   4292  5241 ae010109r1    859 (  0)  0.33 0.00 0.00   52 ( 52)    0 (  0) 
   4500  5476 cc060109f1    884 (  0)  0.63 0.32 0.00   30 ( 30)    1 (  1) 
   5002  5929 bc110109r1    841 (  0)  0.11 0.00 0.00   52 ( 52)    0 (  0) 
   5022  5987 fb060109r1    789 (  0)  1.88 0.77 0.00   62 ( 62)    0 ( 46) 
   5150  6136 ad030109f1    879 (  0)  0.53 0.00 0.21   51 ( 51)    0 (  0) 
   5202  6103 eh010109r1    801 (  0)  0.59 0.00 0.00   50 ( 50)    4 (  3) 
   5221  6143 ea070109r1    748 (  0)  1.89 0.12 0.35   50 ( 50)   25 ( 84) 
   5419  6387 be040109r1    882 (  0)  0.33 0.00 0.00   48 ( 48)    0 (  4) 
   5453  6387 eb110109r1    858 (  0)  0.23 0.00 0.00   48 ( 48)    0 (  0) 
   5649  6639 ac030109r1    872 (  0)  0.44 0.00 0.11   71 ( 71)    3 (  3) 
C  5680  6943 cc060109r1    343 (  0)  2.78 2.55 0.00  782 (811)   51 ( 51) 
   5773  6687 dh010109r1    819 ( 59)  0.58 0.00 0.12   46 ( 46)    1 (  1) 
   5797  6765 ad020109r1    868 (143)  0.22 0.11 0.22   55 ( 55)    0 (  0) 
   5998  6933 ee070109r1    736 (185)  1.71 0.61 0.00   53 ( 53)   64 (107) 
   6001  6969 ef060109r1    832 (245)  1.85 0.11 0.22   47 ( 47)    1 ( 64) 
C  6207  7141 ag010109r1    855 (  0)  0.11 0.11 0.00    0 (  0)   57 ( 57) 
   6313  7271 de090109f1    869 (  0)  1.61 0.21 0.00   26 ( 83)    1 (  1) 
C  6511  7448 ea070109f1    830 ( 64)  1.12 0.45 0.22   13 ( 13)   31 ( 31) 
C  6513  7410 eh010109f1    715 (186)  4.15 0.35 0.58    2 (135)   28 ( 44) 
C  6535  7509 ad030109r1    891 (105)  0.44 0.11 0.00    0 (  0)   59 ( 59) 
C  6561  7478 bc110109f1    873 (102)  0.00 0.00 0.11    0 (  0)   33 ( 29) 
   6576  7514 eh030109f1    860 (245)  0.77 0.55 0.00   30 ( 30)    3 (  3) 
   6678  7619 ca040109f1     43 ( 35)  23.50 4.76 0.61   47 ( 93)  244 (301) 
C  6746  7700 be040109f1    901 (100)  0.43 0.11 0.11    0 (  0)   28 ( 28) 
C  6766  7679 eb110109f1    822 ( 64)  1.35 0.56 0.11    0 ( 20)   26 ( 26) 
C  6823  7795 fb060109f1    907 (  0)  0.53 0.11 0.00    8 (  8)   30 ( 30) 
   6983  7959 ac090109r1    894 (123)  0.54 0.22 0.00   54 ( 54)    1 (  1) 
C  7048  7996 ae010109f1    886 (  0)  0.44 0.00 0.22    0 (  0)   33 ( 33) 
C  7153  8113 ef060109f1    671 (  0)  2.72 1.61 0.25  125 (239)   28 ( 28) 
   7335  8292 fa060109r1    780 ( 48)  2.05 1.03 0.00   46 ( 46)   35 (135) 
   7390  8329 ee020109r1    822 (  0)  0.90 0.11 0.67   50 ( 50)    0 ( 22) 
C  7399  8363 de090109r1    842 (  0)  1.09 0.98 0.00    1 ( 52)   48 ( 48) 
   7413  8383 bc050109r1    848 (  0)  1.19 0.65 0.22   48 ( 48)    1 (  1) 
C  7427  8405 ac030109f1    903 (  0)  0.54 0.00 0.00    2 (  2)   49 ( 49) 
   7440  8415 ag050109r1    876 (  0)  1.09 0.11 0.00   55 ( 55)    1 (  1) 
C  7441  8395 ee070109f1    894 (  0)  0.86 0.00 0.00    0 ( 16)   28 ( 32) 
   7570  8532 ff030109r1    888 (  0)  0.11 0.33 0.00   49 ( 49)    0 (  0) 
   7670  8624 ca070109r1    480 ( 41)  5.86 2.26 0.15   48 ( 64)  242 (375) 
C  7750  8701 ca040109r1    276 (224)  18.95 1.71 0.12   18 (146)  116 (262) 
C  7846  8828 ad020109f1    909 (  0)  0.22 0.00 0.00    0 (  0)   56 ( 56) 
C  8041  8991 ca070109f1    831 (  0)  1.74 0.44 0.11    5 (  5)   29 ( 29) 
C  8215  9170 eh030109r1    874 (  0)  0.33 0.11 0.00    3 (  3)   51 ( 51) 
C  8505  9496 ac090109f1    909 (  0)  0.43 0.00 0.11    0 (  0)   51 ( 51) 
C  8615  9577 ff030109f1    907 (  0)  0.43 0.00 0.00    0 ( 10)   29 ( 29) 
C  8649  9569 ee020109f1    872 (  0)  0.22 0.00 0.00    2 (  2)   28 ( 28) 
C  8914  9854 bc050109f1    809 (  0)  1.85 0.87 0.22    0 ( 35)   24 ( 24) 
C  8968  9934 ag050109f1    909 (  0)  0.43 0.00 0.11    1 (  1)   27 ( 27) 
   9103 10153 dc020109r1    118 (  0)  11.85 4.81 0.00  336 (414)  445 (513) 
   9143 10122 fe050109r1    864 (  0)  1.39 0.32 0.00   45 ( 45)    3 ( 41) 
C  9152 10123 ee040109f1     79 (  0)  21.91 3.68 0.74  100 (360)  192 (284) 
   9396 10360 df080109r1    805 (  0)  1.69 0.67 0.11   47 ( 47)   28 (103) 
   9491 10445 ef020109r1    869 ( 80)  0.88 0.00 0.00   51 ( 51)    0 (  0) 
   9554 10654 ce070109r1    277 (  0)  5.87 0.00 0.00   82 ( 96)  678 (697) 
   9645 10562 eh120109r1    785 (160)  2.08 0.35 0.12   50 ( 50)    1 (  1) 
  10458 11412 da010109r1    728 (245)  2.92 1.17 0.12   57 ( 61)   43 (104) 
C 10521 11484 df080109f1    404 (245)  13.24 0.17 1.19  286 (438)   89 ( 94) 
C 10553 11519 ef020109f1    662 ( 35)  1.23 0.69 0.27  209 (209)   29 ( 29) 
C 10608 11586 fe050109f1    939 ( 35)  0.10 0.00 0.00    0 (  0)   25 ( 25) 
  10674 11651 ac060109r1    883 ( 55)  0.33 0.00 0.00   55 ( 55)   15 ( 15) 
  10726 11652 dd120109f1    862 ( 35)  0.45 0.11 0.00   34 ( 34)    0 (  0) 
C 10963 11860 eh120109f1    770 (236)  2.99 0.00 0.11    3 (  3)   25 ( 25) 
  10964 11886 dg110109f1    174 (  0)  35.80 0.13 0.25  137 (685)    1 (200) 
  11024 11975 ch030109f1    826 (173)  1.73 0.32 0.32   28 ( 28)    0 (  0) 
  11077 12048 ab100109f1    894 (113)  0.11 0.00 0.11   48 ( 48)    0 (  0) 
  11266 12213 ec030109f1    883 (  0)  0.44 0.00 0.00   30 ( 30)    0 (  0) 
C 11273 12245 ce070109f1    902 (  0)  0.52 0.10 0.21    1 (  6)   19 ( 36) 
C 11478 12404 e0111p12sp6_f07  484 (  0)  6.03 1.76 0.15  143 (252)  104 (138) 
  11549 12497 fa090109f1    717 (  0)  0.79 0.00 0.13   28 ( 28)  164 (164) 
  11579 12537 fa040109f1    697 (  0)  0.41 0.14 0.00   29 ( 29)  204 (204) 
  11592 12571 ce040109f1    464 (  0)  7.98 1.31 0.44   31 ( 98)  260 (258) 
C 11740 12727 ac060109f1    543 (  0)  1.52 0.00 0.17    1 ( 34)  394 (394) 
C 12068 12999 dd120109r1    130 (  0)  9.02 5.26 0.00    0 ( 20)  666 (666) 
C 12230 13201 ec030109r1     30 (  0)  5.88 5.88 0.00   52 ( 52)  869 (869) 

Overall discrep rates (%):             2.23 0.40 0.13

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    6128  49.7    6128  49.7    0.00
 89      49   0.4    6177  50.1    0.00
 88      64   0.5    6241  50.6    0.00
 87      44   0.4    6285  51.0    0.00
 86      50   0.4    6335  51.4    0.00
 85      51   0.4    6386  51.8    0.00
 84      46   0.4    6432  52.2    0.00
 83      27   0.2    6459  52.4    0.00
 82      54   0.4    6513  52.8    0.00
 81     102   0.8    6615  53.6    0.00
 80      37   0.3    6652  53.9    0.00
 79      42   0.3    6694  54.3    0.00
 78      28   0.2    6722  54.5    0.00
 77      37   0.3    6759  54.8    0.00
 76      45   0.4    6804  55.2    0.00
 75      52   0.4    6856  55.6    0.00
 74      31   0.3    6887  55.8    0.00
 73      19   0.2    6906  56.0    0.00
 72      22   0.2    6928  56.2    0.00
 71      24   0.2    6952  56.4    0.00
 70      28   0.2    6980  56.6    0.00
 69      31   0.3    7011  56.8    0.00
 68      27   0.2    7038  57.1    0.00
 67      28   0.2    7066  57.3    0.00
 66    1773  14.4    8839  71.7    0.00
 65      15   0.1    8854  71.8    0.00
 64      16   0.1    8870  71.9    0.00
 63      22   0.2    8892  72.1    0.00
 62       9   0.1    8901  72.2    0.00
 61     701   5.7    9602  77.9    0.00
 60     154   1.2    9756  79.1    0.00
 59       6   0.0    9762  79.2    0.00
 58      18   0.1    9780  79.3    0.00
 57      16   0.1    9796  79.4    0.00
 56     156   1.3    9952  80.7    0.00
 55     219   1.8   10171  82.5    0.00
 54     108   0.9   10279  83.3    0.00
 53     365   3.0   10644  86.3    0.00
 52     232   1.9   10876  88.2    0.01
 51     116   0.9   10992  89.1    0.01
 50     176   1.4   11168  90.6    0.01
 49      23   0.2   11191  90.7    0.01
 48      48   0.4   11239  91.1    0.01
 47      32   0.3   11271  91.4    0.01
 46      20   0.2   11291  91.6    0.01
 45      68   0.6   11359  92.1    0.01
 44      58   0.5   11417  92.6    0.02
 43      31   0.3   11448  92.8    0.02
 42     120   1.0   11568  93.8    0.02
 41      31   0.3   11599  94.0    0.03
 40      42   0.3   11641  94.4    0.03
 39      16   0.1   11657  94.5    0.03
 38      34   0.3   11691  94.8    0.04
 37      36   0.3   11727  95.1    0.05
 36      20   0.2   11747  95.2    0.05
 35      75   0.6   11822  95.9    0.07
 34      14   0.1   11836  96.0    0.08
 33      25   0.2   11861  96.2    0.09
 32      25   0.2   11886  96.4    0.11
 31      15   0.1   11901  96.5    0.12
 30      12   0.1   11913  96.6    0.13
 29      28   0.2   11941  96.8    0.17
 28      12   0.1   11953  96.9    0.19
 27      24   0.2   11977  97.1    0.23
 26      12   0.1   11989  97.2    0.26
 25      21   0.2   12010  97.4    0.33
 24      16   0.1   12026  97.5    0.39
 23      22   0.2   12048  97.7    0.50
 22      20   0.2   12068  97.9    0.63
 21      13   0.1   12081  98.0    0.73
 20      12   0.1   12093  98.1    0.85
 19      15   0.1   12108  98.2    1.04
 18      19   0.2   12127  98.3    1.34
 17       8   0.1   12135  98.4    1.50
 16      19   0.2   12154  98.5    1.98
 15      20   0.2   12174  98.7    2.61
 14       9   0.1   12183  98.8    2.97
 13      19   0.2   12202  98.9    3.92
 12      12   0.1   12214  99.0    4.68
 11      26   0.2   12240  99.2    6.75
 10      19   0.2   12259  99.4    8.65
  9      26   0.2   12285  99.6   11.92
  8       8   0.1   12293  99.7   13.19
  7      17   0.1   12310  99.8   16.58
  6       7   0.1   12317  99.9   18.34
 -1      16   0.1   12333 100.0   34.34   (quality -1 = terminal quality 0)

Avg. full length: 12333.0, trimmed (qual > -1): 12317.0
Avg. quality: 73.9 per base

Initial, terminal qual 0 segments:  1-16, (None)

Regions of LLR- adjusted quality < 2.0:
1-20, 37-40, 47-52, 3793-3795, 3811, 3829-3831, 3842-3844, 4175, 
4209-4210, 4234-4237, 4239, 4241-4243, 4245, 4247-4250, 4272, 4285-4286, 
10270-10274, 10276-10278, 10287, 10302-10303, 10318-10326, 10331-10334, 10336-10337, 10340-10341, 
10345-10348, 10352-10358, 10360-10361, 10366-10375, 10377-10402, 10404-10409, 10412-10439, 10441, 
10445-10454, 10459-10479, 10481-10518, 

36 regions, avg size 6.7, avg spacing 342.6

First_start: 17, last_end: 12333

Slack, # used pairs (max_score), unused
 0   285  (20.1)     0 ( 0.0)      753
 1   260  (19.8)     0 ( 0.0)       91
 2    65  (18.7)     0 ( 0.0)        0
 3    35  (19.1)     0 ( 0.0)        0
 4    18  (18.3)     0 ( 0.0)        0
 5    10  (15.6)     0 ( 0.0)        0
 6    12  (18.8)     0 ( 0.0)        0
 7     5  (11.0)     0 ( 0.0)        0
 8     5  (18.1)     0 ( 0.0)        0
 9     1  (14.8)     0 ( 0.0)        0
10     1  (11.0)     0 ( 0.0)        0
11     1  ( 7.1)     0 ( 0.0)        0
12     1  (11.0)     0 ( 0.0)        0
13     1  (11.0)     0 ( 0.0)        0
99     0  ( 0.0)   144 ( 6.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 2851 -  4266     1416       fg110109f1   (1934)    No           2333
 8533 -  9187      655       ca070109r1   (7670)    No           1518
12334 - right        0+      ce040109f1   (11592)    No            741+

Bottom strand: 
 left -   863      863+      ad070109r1   (1850)    No           1850+
 5019 -  6206     1188       cc060109r1   (6943)    No           1925 
 9932 - 10607      676       df080109f1   (11484)    No           1553 
12334 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  11774  11774  87879 (100.00)     0  0    0   0   0   0     0 (0.00)    0  2410 (2.74)
51   6529  18303  76105 ( 86.60)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.17)
50   2124  20427  69576 ( 79.17)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.46)
48    358  20785  67452 ( 76.76)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.57)
47    271  21056  67094 ( 76.35)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.59)
46   1330  22386  66823 ( 76.04)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.61)
45   2507  24893  65493 ( 74.53)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.68)
44   1615  26508  62986 ( 71.67)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.83)
43   4115  30623  61371 ( 69.84)     0  0    0   0   0   0     0 (0.00)    0  2410 (3.93)
42   5290  35913  57256 ( 65.15)     1  0    0   0   0   0     0 (0.00)    0  2410 (4.21)
41   1528  37441  51966 ( 59.13)     0  0    0   0   0   0     0 (0.00)    0  2410 (4.64)
40   5142  42583  50438 ( 57.39)    18  0    0   2   0   0     2 (0.04)    2  2410 (4.78)
39    497  43080  45296 ( 51.54)     1  0    0   0   0   0     0 (0.00)    2  2408 (5.32)
38    801  43881  44799 ( 50.98)     0  0    0   0   0   0     0 (0.00)    2  2408 (5.38)
37   2120  46001  43998 ( 50.07)     3  0    0   0   0   0     0 (0.00)    2  2408 (5.47)
36    374  46375  41878 ( 47.65)     0  0    0   0   0   0     0 (0.00)    2  2408 (5.75)
35   3266  49641  41504 ( 47.23)     9  0    0   0   0   0     0 (0.00)    2  2408 (5.80)
34    715  50356  38238 ( 43.51)    11  0    0   0   0   0     0 (0.00)    2  2408 (6.30)
33   1229  51585  37523 ( 42.70)     3  0    0   1   0   0     1 (0.08)    3  2408 (6.42)
32   1174  52759  36294 ( 41.30)    15  0    0   1   0   0     1 (0.09)    4  2407 (6.63)
31    540  53299  35120 ( 39.96)     2  0    0   0   0   0     0 (0.00)    4  2406 (6.85)
30    660  53959  34580 ( 39.35)     4  0    0   0   0   0     0 (0.00)    4  2406 (6.96)
29   2102  56061  33920 ( 38.60)    27  0    0   0   4   0     4 (0.19)    8  2406 (7.09)
28    711  56772  31818 ( 36.21)     3  0    0   2   0   0     2 (0.28)   10  2402 (7.55)
27   1079  57851  31107 ( 35.40)    22  0    0   1   0   0     1 (0.09)   11  2400 (7.72)
26    478  58329  30028 ( 34.17)    13  0    0   0   1   0     1 (0.21)   12  2399 (7.99)
25   1254  59583  29550 ( 33.63)    26  0    0   0   0   0     0 (0.00)   12  2398 (8.12)
24   1012  60595  28296 ( 32.20)    26  0    0   0   0   0     0 (0.00)   12  2398 (8.47)
23    837  61432  27284 ( 31.05)    19  0    0   1   2   0     3 (0.36)   15  2398 (8.79)
22    837  62269  26447 ( 30.09)    35  0    0   3   1   0     4 (0.48)   19  2395 (9.06)
21    979  63248  25610 ( 29.14)     6  0    0   4   2   0     6 (0.61)   25  2391 (9.34)
20    821  64069  24631 ( 28.03)    29  0    0   3   4   1     8 (0.97)   33  2385 (9.68)
19   1473  65542  23810 ( 27.09)    56  0    0   7   0   0     7 (0.48)   40  2377 (9.98)
18    873  66415  22337 ( 25.42)    19  0    0   5   5   1    11 (1.26)   51  2370 (10.61)
17    985  67400  21464 ( 24.42)    27  0    0  10   5   0    15 (1.52)   66  2359 (10.99)
16   1103  68503  20479 ( 23.30)    44  0    0  20  10   0    30 (2.72)   96  2344 (11.45)
15   1257  69760  19376 ( 22.05)    26  0    0  21   5   0    26 (2.07)  122  2314 (11.94)
14   1193  70953  18119 ( 20.62)    34  0    0  39   9   3    51 (4.27)  173  2288 (12.63)
13   1627  72580  16926 ( 19.26)    30  0    0  74  16   4    94 (5.78)  267  2237 (13.22)
12   1448  74028  15299 ( 17.41)    20  0    0  78  11   2    91 (6.28)  358  2143 (14.01)
11   2162  76190  13851 ( 15.76)    29  0    0 157  24   7   188 (8.70)  546  2052 (14.81)
10   2668  78858  11689 ( 13.30)    54  0    0 215  28  16   259 (9.71)  805  1864 (15.95)
 9   3910  82768   9021 ( 10.27)   129  0    0 390  78  39   507 (12.97)  1312  1605 (17.79)
 8   2069  84837   5111 (  5.82)    85  0    0 250  56  17   323 (15.61)  1635  1098 (21.48)
 7   1566  86403   3042 (  3.46)    32  0    0 221  43  10   274 (17.50)  1909  775 (25.48)
 6    854  87257   1476 (  1.68)    42  0    0 132  39   5   176 (20.61)  2085  501 (33.94)
 4    364  87621    622 (  0.71)    11  0    0  57   3   1    61 (16.76)  2146  325 (52.25)
 0    258  87879    258 (  0.29)     0  0   258   0   0   6   264 (102.33)  2410  264 (102.33)
-1     16  87895      0 (  0.00)  8686  0    0   0   0   0     0 (0.00)  2410    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  46280  46280  83739 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1310 (1.56)
89    306  46586  37459 ( 44.73)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.50)
88    350  46936  37153 ( 44.37)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.53)
87    239  47175  36803 ( 43.95)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.56)
86    230  47405  36564 ( 43.66)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.58)
85    255  47660  36334 ( 43.39)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.61)
84    206  47866  36079 ( 43.09)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.63)
83    139  48005  35873 ( 42.84)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.65)
82    237  48242  35734 ( 42.67)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.67)
81    549  48791  35497 ( 42.39)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.69)
80    175  48966  34948 ( 41.73)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.75)
79    139  49105  34773 ( 41.53)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.77)
78    101  49206  34634 ( 41.36)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.78)
77     93  49299  34533 ( 41.24)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.79)
76    156  49455  34440 ( 41.13)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.80)
75    161  49616  34284 ( 40.94)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.82)
74     54  49670  34123 ( 40.75)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.84)
73     79  49749  34069 ( 40.68)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.85)
72     58  49807  33990 ( 40.59)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.85)
71     80  49887  33932 ( 40.52)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.86)
70    100  49987  33852 ( 40.43)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.87)
69    114  50101  33752 ( 40.31)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.88)
68     67  50168  33638 ( 40.17)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.89)
67    110  50278  33571 ( 40.09)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.90)
66  10128  60406  33461 ( 39.96)     0  0    0   0   0   0     0 (0.00)    0  1310 (3.92)
65     90  60496  23333 ( 27.86)     0  0    0   0   0   0     0 (0.00)    0  1310 (5.61)
64     54  60550  23243 ( 27.76)     0  0    0   0   0   0     0 (0.00)    0  1310 (5.64)
63     38  60588  23189 ( 27.69)     0  0    0   0   0   0     0 (0.00)    0  1310 (5.65)
62     44  60632  23151 ( 27.65)     0  0    0   0   0   0     0 (0.00)    0  1310 (5.66)
61   3942  64574  23107 ( 27.59)     0  0    0   0   0   0     0 (0.00)    0  1310 (5.67)
60    730  65304  19165 ( 22.89)     0  0    0   0   0   0     0 (0.00)    0  1310 (6.84)
59     37  65341  18435 ( 22.01)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.11)
58     76  65417  18398 ( 21.97)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.12)
57     80  65497  18322 ( 21.88)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.15)
56    699  66196  18242 ( 21.78)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.18)
55   1091  67287  17543 ( 20.95)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.47)
54    546  67833  16452 ( 19.65)     0  0    0   0   0   0     0 (0.00)    0  1310 (7.96)
53   1806  69639  15906 ( 18.99)     0  0    0   0   0   0     0 (0.00)    0  1310 (8.24)
52    901  70540  14100 ( 16.84)     0  0    0   0   0   0     0 (0.00)    0  1310 (9.29)
51    554  71094  13199 ( 15.76)     0  0    0   0   0   0     0 (0.00)    0  1310 (9.92)
50    621  71715  12645 ( 15.10)     0  0    0   0   0   0     0 (0.00)    0  1310 (10.36)
49    125  71840  12024 ( 14.36)     0  0    0   0   0   0     0 (0.00)    0  1310 (10.89)
48    217  72057  11899 ( 14.21)     0  0    0   0   0   0     0 (0.00)    0  1310 (11.01)
47    134  72191  11682 ( 13.95)     0  0    0   0   0   0     0 (0.00)    0  1310 (11.21)
46    127  72318  11548 ( 13.79)     0  0    0   0   0   0     0 (0.00)    0  1310 (11.34)
45    267  72585  11421 ( 13.64)     0  0    0   0   0   0     0 (0.00)    0  1310 (11.47)
44    251  72836  11154 ( 13.32)     0  0    0   0   0   0     0 (0.00)    0  1310 (11.74)
43    168  73004  10903 ( 13.02)     0  0    0   0   0   0     0 (0.00)    0  1310 (12.02)
42    270  73274  10735 ( 12.82)     0  0    0   0   0   0     0 (0.00)    0  1310 (12.20)
41    195  73469  10465 ( 12.50)     0  0    0   0   0   0     0 (0.00)    0  1310 (12.52)
40   1911  75380  10270 ( 12.26)     0  0    0   1   0   0     1 (0.05)    1  1310 (12.76)
39     84  75464   8359 (  9.98)     0  0    0   0   0   0     0 (0.00)    1  1309 (15.66)
38     74  75538   8275 (  9.88)     0  0    0   0   0   0     0 (0.00)    1  1309 (15.82)
37    100  75638   8201 (  9.79)     0  0    0   0   1   0     1 (1.00)    2  1309 (15.96)
36     71  75709   8101 (  9.67)     0  0    0   0   0   0     0 (0.00)    2  1308 (16.15)
35    128  75837   8030 (  9.59)     0  0    0   0   0   0     0 (0.00)    2  1308 (16.29)
34     89  75926   7902 (  9.44)     1  0    0   0   0   0     0 (0.00)    2  1308 (16.55)
33     80  76006   7813 (  9.33)     0  0    0   1   0   0     1 (1.25)    3  1308 (16.74)
32     85  76091   7733 (  9.23)     0  0    0   0   0   0     0 (0.00)    3  1307 (16.90)
31     56  76147   7648 (  9.13)     0  0    0   0   0   0     0 (0.00)    3  1307 (17.09)
30     46  76193   7592 (  9.07)     0  0    0   0   0   0     0 (0.00)    3  1307 (17.22)
29    141  76334   7546 (  9.01)     2  0    0   0   4   0     4 (2.84)    7  1307 (17.32)
28     53  76387   7405 (  8.84)     0  0    0   1   0   0     1 (1.89)    8  1303 (17.60)
27     88  76475   7352 (  8.78)     0  0    0   1   0   0     1 (1.14)    9  1302 (17.71)
26     72  76547   7264 (  8.67)     0  0    0   0   1   0     1 (1.39)   10  1301 (17.91)
25    521  77068   7192 (  8.59)     0  0    0   1   0   0     1 (0.19)   11  1300 (18.08)
24     99  77167   6671 (  7.97)     1  0    0   1   0   0     1 (1.01)   12  1299 (19.47)
23     94  77261   6572 (  7.85)     1  0    0   1   1   0     2 (2.13)   14  1298 (19.75)
22     74  77335   6478 (  7.74)     0  0    0   2   1   0     3 (4.05)   17  1296 (20.01)
21     94  77429   6404 (  7.65)     0  0    0   4   2   0     6 (6.38)   23  1293 (20.19)
20     91  77520   6310 (  7.54)     0  0    0   2   3   1     6 (6.59)   29  1287 (20.40)
19    176  77696   6219 (  7.43)     3  0    0   6   0   0     6 (3.41)   35  1281 (20.60)
18     86  77782   6043 (  7.22)     0  0    0   5   3   1     9 (10.47)   44  1275 (21.10)
17    143  77925   5957 (  7.11)     1  0    0   8   3   0    11 (7.69)   55  1266 (21.25)
16    214  78139   5814 (  6.94)     0  0    0  12   8   0    20 (9.35)   75  1255 (21.59)
15    218  78357   5600 (  6.69)     0  0    0  15   4   1    20 (9.17)   95  1235 (22.05)
14    229  78586   5382 (  6.43)     0  0    0  28   6   3    37 (16.16)  132  1215 (22.58)
13    377  78963   5153 (  6.15)     0  0    0  47   9   3    59 (15.65)  191  1178 (22.86)
12    344  79307   4776 (  5.70)     0  0    0  41   7   2    50 (14.53)  241  1119 (23.43)
11    617  79924   4432 (  5.29)     0  0    0 101  11   5   117 (18.96)  358  1069 (24.12)
10    811  80735   3815 (  4.56)     0  0    0 130  21   9   160 (19.73)  518  952 (24.95)
 9   1291  82026   3004 (  3.59)     0  0    0 203  51  27   281 (21.77)  799  792 (26.36)
 8    653  82679   1713 (  2.05)     4  0    0 144  34  12   190 (29.10)  989  511 (29.83)
 7    652  83331   1060 (  1.27)     0  0    0 154  32   8   194 (29.75)  1183  321 (30.28)
 6    344  83675    408 (  0.49)     1  0    0  83  21   1   105 (30.52)  1288  127 (31.13)
 4     51  83726     64 (  0.08)     0  0    0   7   2   0     9 (17.65)  1297   22 (34.38)
 0     13  83739     13 (  0.02)     0  0   13   0   0   0    13 (100.00)  1310   13 (100.00)
-1   4156  87895      0 (  0.00)  9583  0   245 695 121  39   1100 (26.47)  2410    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      16       16        1
  6       7       23        4
  7      17       40        7
  8       8       48        9
  9      26       74       21
 10      19       93       24
 11      26      119       30
 12      12      131       30
 13      19      150       31
 14       9      159       32
 15      20      179       38
 16      19      198       36
 17       8      206       34
 18      19      225       36
 19      15      240       35
 20      12      252       36
 21      13      265       37
 22      20      285       43
 23      22      307       42
 24      16      323       42
 25      21      344       42
 26      12      356       45
 27      24      380       41
 28      12      392       38
 29      28      420       41
 30      12      432       40
 31      15      447       37
 32      25      472       40
 33      25      497       41
 34      14      511       46
 35      75      586       56
 36      20      606       58
 37      36      642       63
 38      34      676       72
 39      16      692       70
 40      42      734       75
 41      31      765       76
 42     120      885       69
 43      31      916       63
 44      58      974       66
 45      68     1042       75
 46      20     1062       75
 47      32     1094       78
 48      48     1142       92
 49      23     1165       95
 50     176     1341      104
 51     116     1457      142
 52     232     1689      205
 53     365     2054      265
 54     108     2162      279
 55     219     2381      278
 56     156     2537      256
 57      16     2553      258
 58      18     2571      254
 59       6     2577      255
 60     154     2731      248
 61     701     3432      276
 62       9     3441      276
 63      22     3463      284
 64      16     3479      286
 65      15     3494      284
 66    1773     5267       61
 67      28     5295       63
 68      27     5322       71
 69      31     5353       77
 70      28     5381       80
 71      24     5405       84
 72      22     5427       82
 73      19     5446       81
 74      31     5477       88
 75      52     5529       84
 76      45     5574       91
 77      37     5611       92
 78      28     5639       93
 79      42     5681       91
 80      37     5718       95
 81     102     5820      105
 82      54     5874      108
 83      27     5901      104
 84      46     5947      103
 85      51     5998      112
 86      50     6048      116
 87      44     6092      121
 88      64     6156      131
 89      49     6205      131
 90    6128    12333        1

SS region: 4798 (38.90%), flagged: 3 (0.02%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 1610     -5.1  [-2.8,  0.0]  (0, 2)
 4234     -4.0  [-4.0,  0.0]  (0, 1)
 4236     -3.2  [-3.2,  0.0]  (0, 1)
 6633     -4.0  [-4.0,  0.0]  (0, 1)
 7306     -3.6  [-2.0,  0.0]  (0, 2)
 9542     -3.4  [-3.4,  0.0]  (0, 1)
 9549     -3.4  [-3.4,  0.0]  (0, 1)
10973     -3.3  [-3.3,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  6725- 7375 [-11.9] (0,0)     ca040109f1         48-725 || local(+/-) (11.0,0.0), distant (1.8,0.0)
LLR breakdown: discreps: -21.2 (<20 part: -21.2 (#=188), >20:0.0 (#=0); in HQ: 0.0, out HQ -21.2), match: 9.3  trail: 0.0  lead: 0.0  total: -11.9 
(0, 0)  7768- 8585 [-6.4] (0,0)   C ca040109r1         947-117 || local(+/-) (12.6,0.0), distant (1.8,0.0)
LLR breakdown: discreps: -16.7 (<20 part: -16.7 (#=170), >20:0.0 (#=0); in HQ: 0.0, out HQ -16.7), match: 10.3  trail: 0.0  lead: 0.0  total: -6.4 
(0, 0)  9252- 9931 [-4.1] (0,0)   C ee040109f1         892-193 || local(+/-) (10.7,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -10.1 (<20 part: -10.1 (#=179), >20:0.0 (#=0); in HQ: 0.0, out HQ -10.1), match: 6.0  trail: 0.0  lead: 0.0  total: -4.1 
(0, 0)  9695-10561 [14.9] (0,0)     eh120109r1         51-919 | 51 919 | DA:(804 872) || local(+/-) (15.6,2.9), distant (2.6,0.0)
(7, 0) 10515-11369 [11.9] (0,0)     da010109r1         58-921 | 48 921 | DA:(**48 57**)(**105 150**) || local(+/-) (15.7,0.0), distant (5.7,0.0)
(0, 0) 10762-11490 [13.0] (0,0)   C ef020109f1         761-30 | 30 829 | DA:(762 829) || local(+/-) (14.9,0.0), distant (0.0,1.6)
(0, 0) 12068-12333 [-0.3] (0,0)   C dd120109r1         946-667 || local(+/-) (5.2,1.1), distant (0.0,0.0)
LLR breakdown: discreps: -5.4 (<20 part: -5.4 (#=38), >20:0.0 (#=0); in HQ: -1.6, out HQ -3.8), match: 5.0  total: -0.4 
(0, 0) 12282-12332 [-0.9] (0,0)   C ec030109r1         923-870 || local(+/-) (1.0,1.1), distant (0.0,0.0)
LLR breakdown: discreps: -2.0 (<20 part: -2.0 (#=6), >20:0.0 (#=0); in HQ: 0.0, out HQ -2.0), match: 1.1  trail: 0.0  lead: 0.0  total: -0.9 

Gaps in unique-read coverage:   I 3754- 4270, I 10258- 11278

Contig 10.  111 reads; 9816 bp (untrimmed), 9786 (trimmed).  Isolated contig.
   -680   288 af090109f1    146 (  0)  12.64 1.08 0.00  681 (681)   11 (143) 
   -573   364 eb090109f1    239 (  0)  8.79 0.82 0.27  574 (574)    0 ( 16) 
   -394   562 ch070109f1    492 (  0)  1.78 0.71 0.18  395 (395)    0 (  0) 
C  -321   651 af040109f1    569 (  0)  1.30 0.16 0.00  323 (323)   35 ( 35) 
C  -204   765 ae100109f1    699 (  0)  0.28 0.00 0.00  205 (205)   40 ( 39) 
    -96   957 ae100109r1    311 (  0)  12.59 0.19 0.00  282 (368)  232 (231) 
    -35   944 bd010109r1    534 (  0)  2.92 0.32 0.16  362 (389)    1 (  0) 
    -29   971 ac050109r1    651 (  0)  4.66 0.96 0.36  154 (187)   10 (  7) 
    -11   959 af090109r1    232 (  0)  19.05 2.33 0.78   68 (296)    0 (138) 
    -12   947 cb100109r1    361 (  0)  12.78 2.08 0.00  206 (341)   34 ( 22) 
    -15   924 df120109r1    457 (  0)  9.05 0.57 0.43  243 (294)    1 (  1) 
     -9   932 eb090109r1     41 (  0)  25.06 2.73 0.46  224 (558)  279 (365) 
    -15   963 af040109r1    140 (  0)  18.30 0.77 0.26  244 (406)  347 (402) 
     -8   967 ff090109r1     71 (  0)  23.06 2.52 0.54  214 (266)  207 (207) 
    -11   954 eh070109r1    743 (  0)  0.95 1.55 0.00  126 (124)    0 ( 22) 
    -10  1058 cf080109r1    108 (  0)  15.24 0.48 0.00  102 (102)  757 (757) 
C   -11   950 cd040109f1    891 (  0)  0.54 0.00 0.00   12 ( 12)   25 ( 23) 
     -7   979 ff040109r1     44 (  0)  26.19 0.68 0.34  286 (486)  407 (484) 
     -3   959 ch070109r1    177 (  0)  20.50 1.16 0.33  182 (284)  176 (279) 
     -5  1025 cd040109r1    307 (  0)  8.49 1.27 0.42  114 (114)  446 (553) 
      1   949 cc010109r1    574 (  0)  7.11 0.39 0.13  175 (285)    0 (  0) 
     16   946 ce020109r1    433 (  0)  11.83 0.67 0.27  187 (253)    0 (  0) 
C    21   996 ac050109f1    894 (  0)  0.64 0.11 0.11    0 ( 18)   35 ( 32) 
     26  1009 ah080109f1    901 (  0)  0.43 0.11 0.11   43 ( 48)    1 (  1) 
     63   999 bg030109f1    848 (  0)  0.78 0.22 0.11   29 ( 29)    7 (  2) 
    233  1217 ae060109r1    871 (  0)  0.86 0.32 0.00   52 ( 52)    0 (  0) 
    391  1402 de040109r1    507 (  0)  5.38 0.77 0.31   57 ( 80)  305 (386) 
C   414  1363 cc010109f1    868 (  0)  0.76 0.11 0.11    0 (  5)   29 ( 29) 
    521  1483 dh070109r1    870 (  0)  0.44 0.00 0.33   45 ( 45)    0 (  0) 
    614  1541 cd120109r1    827 (  0)  0.80 0.00 0.11   49 ( 61)    8 (  8) 
C   706  1635 bd010109f1    874 (  0)  0.22 0.11 0.00    0 (  0)   29 ( 29) 
    713  1680 ae090109r1    120 (  0)  11.41 0.00 0.00   82 (157)  702 (702) 
    771  1720 ad010109f1    866 (  0)  0.76 0.33 0.11   27 ( 49)    0 (  0) 
C   824  1774 bg030109r1    872 (  0)  0.33 0.00 0.00    0 (  0)   50 ( 50) 
    835  1780 ce010109f1    853 (  0)  1.09 0.44 0.00   27 ( 26)    0 ( 16) 
C   966  1909 ce020109f1    855 (  0)  0.88 0.11 0.00    0 (  0)   34 ( 34) 
   1038  1998 df090109f1    678 (  0)  5.94 0.35 0.35   83 (152)   20 (110) 
C  1394  2384 ah080109r1    870 (  0)  0.22 0.22 0.00    0 (  0)   72 ( 72) 
   1618  2563 aa100109f1    850 (  0)  0.33 0.00 0.11   39 ( 39)    1 (  0) 
C  1756  2709 ad010109r1    858 (  0)  0.33 0.11 0.00    0 (  0)   53 ( 53) 
C  1780  2777 ae060109f1    881 (  0)  0.42 0.42 0.21    1 (  1)   49 ( 49) 
   1902  2864 bc030109r1    843 (  0)  1.10 0.33 0.11   49 ( 49)    1 ( 16) 
C  1946  2922 de040109f1    893 (  0)  0.53 0.32 0.00    4 (  4)   29 ( 29) 
   1970  2898 bb100109f1    876 (  0)  0.11 0.00 0.00   29 ( 29)    0 (  0) 
   2087  3014 dc120109r1    828 (  0)  0.80 0.34 0.00   49 ( 49)    0 (  4) 
   2106  3024 ba100109f1    854 (  0)  0.56 0.00 0.00   27 ( 27)    0 (  0) 
   2144  3105 af020109r1    866 (  0)  0.22 0.00 0.22   59 ( 59)    0 (  0) 
C  2160  3098 ca100109f1    824 (  0)  1.54 0.11 0.33    0 (  4)   28 ( 28) 
C  2260  3189 eh070109f1    842 (  0)  0.66 0.11 0.44    0 (  0)   22 ( 42) 
C  2512  3424 cd120109f1    815 (  0)  0.56 0.00 0.56    0 ( 20)   28 ( 28) 
   2673  3619 eg090109r1    844 (  0)  0.45 0.00 0.11   52 ( 52)    0 (  0) 
C  2712  3674 df090109r1    840 (  0)  0.98 0.44 0.00    0 ( 32)   47 ( 47) 
   2806  3747 ca090109f1    815 (  0)  1.01 0.11 0.11   22 ( 22)   29 ( 33) 
C  2811  3751 ce010109r1    781 (  0)  1.59 0.23 0.11   12 ( 25)   50 ( 50) 
   2825  3793 fb070109f1    883 (  0)  0.21 0.11 0.11   29 ( 29)    0 (  0) 
C  2829  3775 ca090109r1    775 (  0)  2.24 0.11 0.22    1 ( 12)   55 ( 61) 
   2953  3898 ab110109f1    860 (  0)  0.55 0.00 0.00   34 ( 45)    0 (  0) 
   3084  4061 dc060109r1    819 (  0)  2.26 0.11 0.21   47 ( 56)    0 ( 44) 
   3084  4052 ce060109f1    891 (  0)  0.53 0.00 0.11   21 ( 21)    0 (  0) 
C  3228  4161 ba100109r1    842 (  0)  0.11 0.00 0.11    2 (  2)   50 ( 50) 
C  3240  4186 aa100109r1    846 (  0)  0.34 0.00 0.11    2 (  2)   55 ( 55) 
   3261  4232 cc050109f1    868 (  0)  0.74 0.53 0.11   27 ( 27)    0 ( 39) 
   3372  4336 cb080109f1    878 (  0)  0.75 0.00 0.21   34 ( 34)    0 ( 11) 
C  3420  4361 bb100109r1    868 (  0)  0.11 0.11 0.00    0 (  0)   47 ( 47) 
C  3491  4441 bc030109f1    899 (  0)  0.11 0.00 0.00    0 (  0)   30 ( 30) 
C  3498  4446 af020109f1    891 (  0)  0.43 0.00 0.00    0 (  0)   26 ( 26) 
   3756  4678 fg010109r1    837 (  0)  0.23 0.00 0.12   51 ( 51)    9 (  9) 
C  3884  4846 fb070109r1    883 (  0)  0.33 0.22 0.11    0 (  0)   46 ( 46) 
C  3930  4864 eg090109f1    811 (  0)  1.98 0.33 0.33    1 ( 59)   25 ( 34) 
C  4123  5127 ce060109r1    280 (  0)  11.35 0.66 0.22  528 (633)   19 ( 50) 
C  4298  5285 cb080109r1    433 (  0)  5.94 0.70 0.52  370 (425)   46 ( 93) 
   4345  5294 fa060109f1    850 (  0)  1.42 0.44 0.00   29 ( 29)    4 (  4) 
   4362  5306 ca020109f1    885 (  0)  0.76 0.00 0.00   26 ( 26)    3 (  3) 
   4412  5330 ee010109f1    874 (  0)  0.22 0.00 0.00   29 ( 29)    1 (  1) 
C  4698  5694 cc050109r1    445 (  0)  4.89 1.22 0.35  378 (408)   46 ( 46) 
   5063  6033 dd070109r1    896 (  0)  0.33 0.00 0.00   55 ( 55)    3 (  3) 
   5070  6005 ca110109r1    844 (  0)  1.13 0.00 0.11   49 ( 49)    0 (  0) 
C  5087  6051 eb030109r1    905 (  0)  0.11 0.00 0.00    3 (  3)   47 ( 47) 
C  5094  6053 ab110109r1    863 (  0)  0.11 0.11 0.00    3 (  3)   80 ( 79) 
   5193  6136 bf070109f1    903 (  0)  0.11 0.00 0.00   29 ( 29)    0 (  0) 
C  5435  6349 fg010109f1    872 (  0)  0.00 0.11 0.11    0 (  0)   25 ( 25) 
C  5749  6694 ca020109r1    821 (  0)  1.89 0.00 0.11    0 ( 18)   48 ( 62) 
C  5859  6801 ee010109r1    848 (  0)  0.11 0.00 0.00    0 (  0)   63 ( 63) 
   5865  6812 bh090109r1    860 (  0)  0.22 0.00 0.00   49 ( 49)    3 (  3) 
   5906  6856 bh040109r1    876 (  0)  0.00 0.00 0.00   46 ( 46)    0 (  0) 
   6154  7076 cg010109r1    826 (  0)  0.46 0.00 0.00   47 ( 47)    0 (  0) 
   6303  7251 ef040109f1    860 (  0)  0.22 0.00 0.00   34 ( 34)    0 (  0) 
C  6340  7309 db110109r1    467 (  0)  4.38 0.51 0.17  330 (343)   47 ( 47) 
   6458  7427 dh060109r1    873 (  0)  0.11 0.00 0.00   50 ( 50)    0 (  0) 
   6481  7433 eh090109r1    825 (  0)  0.78 0.11 0.11   51 ( 53)    2 (  2) 
   6522  7511 fg060109r1    833 (  0)  0.76 0.54 0.00   65 ( 64)    5 (  0) 
   6557  7496 ee100109f1    762 (  0)  2.32 0.66 0.22   30 ( 29)    4 ( 78) 
   6848  7799 bc040109f1    777 (  0)  1.73 0.35 0.00   29 ( 29)   56 ( 56) 
C  7009  7961 bf070109r1    810 (  0)  2.21 0.33 0.00    0 ( 18)   50 ( 50) 
   7024  7980 cf110109f1    643 (  0)  0.59 0.15 0.00   29 ( 29)  245 (245) 
C  7055  8062 eh090109f1    375 (  0)  4.55 0.65 0.00  517 (581)   29 ( 29) 
   7057  7969 cf120109f1    615 (  0)  0.46 0.15 0.00   29 ( 29)  234 (246) 
C  7062  7994 bh090109f1    817 (  0)  1.56 0.22 0.22    3 (  8)   31 ( 31) 
   7160  8122 bh080109r1    498 (  0)  0.57 0.00 0.19   46 ( 46)  387 (387) 
C  7228  8201 dd070109f1    812 (  0)  2.16 0.43 0.22   19 ( 19)   29 ( 62) 
C  7339  8273 bh040109f1    788 (  0)  2.44 0.55 0.11    4 ( 71)   29 ( 29) 
C  7415  8384 fg060109f1    826 (  0)  2.23 0.21 0.42    0 ( 24)   28 ( 28) 
C  7507  8430 cg010109f1    729 (  0)  3.39 1.13 0.00   12 (138)   28 ( 28) 
C  7591  8528 ca110109f1    765 (  0)  1.72 0.92 0.11   36 (122)   30 ( 30) 
C  7856  8820 ef040109r1    858 (  0)  0.33 0.00 0.11    1 (  1)   49 ( 49) 
C  7986  8951 bc040109r1    832 (  0)  0.98 0.33 0.00    1 (  1)   50 ( 50) 
C  8248  9130 cf120109r1    693 (  0)  2.17 0.72 0.36    4 (  4)   51 ( 51) 
C  8381  9316 cf110109r1    793 (  0)  1.01 0.68 0.00    0 (  0)   49 ( 49) 
C  8448  9409 da060109r1    864 (  0)  0.33 0.00 0.00    2 ( 11)   47 ( 47) 
C  8706  9657 bh080109f1    776 (  0)  1.15 0.92 0.00   54 ( 54)   28 ( 28) 
C  8907  9866 ee100109r1    866 (  0)  0.33 0.00 0.00    0 (  0)   50 (237) 

Overall discrep rates (%):             2.38 0.32 0.12

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    6742  68.7    6742  68.7    0.00
 89      90   0.9    6832  69.6    0.00
 88      66   0.7    6898  70.3    0.00
 87      77   0.8    6975  71.1    0.00
 86      33   0.3    7008  71.4    0.00
 85      68   0.7    7076  72.1    0.00
 84      59   0.6    7135  72.7    0.00
 83      42   0.4    7177  73.1    0.00
 82      43   0.4    7220  73.6    0.00
 81      90   0.9    7310  74.5    0.00
 80      20   0.2    7330  74.7    0.00
 79      29   0.3    7359  75.0    0.00
 78      28   0.3    7387  75.3    0.00
 77      23   0.2    7410  75.5    0.00
 76      42   0.4    7452  75.9    0.00
 75      27   0.3    7479  76.2    0.00
 74      16   0.2    7495  76.4    0.00
 73      14   0.1    7509  76.5    0.00
 72      11   0.1    7520  76.6    0.00
 71       9   0.1    7529  76.7    0.00
 70      20   0.2    7549  76.9    0.00
 69      15   0.2    7564  77.1    0.00
 68      10   0.1    7574  77.2    0.00
 67       7   0.1    7581  77.2    0.00
 66     905   9.2    8486  86.5    0.00
 65       4   0.0    8490  86.5    0.00
 64       3   0.0    8493  86.5    0.00
 63       2   0.0    8495  86.5    0.00
 62       1   0.0    8496  86.6    0.00
 61     315   3.2    8811  89.8    0.00
 60     113   1.2    8924  90.9    0.00
 59       2   0.0    8926  90.9    0.00
 58       3   0.0    8929  91.0    0.00
 57      10   0.1    8939  91.1    0.00
 56     114   1.2    9053  92.2    0.00
 55      79   0.8    9132  93.0    0.00
 54      38   0.4    9170  93.4    0.00
 53     216   2.2    9386  95.6    0.00
 52     128   1.3    9514  96.9    0.00
 51     109   1.1    9623  98.0    0.00
 50      43   0.4    9666  98.5    0.00
 49       1   0.0    9667  98.5    0.00
 48      13   0.1    9680  98.6    0.00
 47      20   0.2    9700  98.8    0.01
 46       6   0.1    9706  98.9    0.01
 45      25   0.3    9731  99.1    0.01
 43      19   0.2    9750  99.3    0.01
 42       7   0.1    9757  99.4    0.01
 41       6   0.1    9763  99.5    0.01
 40       8   0.1    9771  99.5    0.01
 39       5   0.1    9776  99.6    0.01
 35      10   0.1    9786  99.7    0.01
 -1      30   0.3    9816 100.0   30.01   (quality -1 = terminal quality 0)

Avg. full length: 9816.0, trimmed (qual > -1): 9786.0
Avg. quality: 82.2 per base

Initial, terminal qual 0 segments:  (None), 9787-9816

Regions of LLR- adjusted quality < 2.0:
9787-9816, 

1 regions, avg size 30.0, avg spacing 9816.0

First_start: 1, last_end: 9629

Slack, # used pairs (max_score), unused
 0   474  (20.2)     0 ( 0.0)      946
 1   361  (19.8)     0 ( 0.0)       54
 2    85  (18.5)     0 ( 0.0)        1
 3    25  (18.8)     0 ( 0.0)        0
 4    17  ( 8.6)     0 ( 0.0)        0
 5    16  ( 7.3)     0 ( 0.0)        0
 6    14  ( 8.8)     0 ( 0.0)        0
 7     8  ( 9.4)     0 ( 0.0)        0
 8     1  ( 6.0)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 7744 - right     2073+      bh080109r1   (7160)    No           2656+

Bottom strand: 
 left -     0        0+      af040109f1   ( 651)    Yes           651+
 9817 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  11108  11108  90132 (100.00)     0  0    0   0   0   0     0 (0.00)    0  2543 (2.82)
51   5792  16900  79024 ( 87.68)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.22)
50   2570  19470  73232 ( 81.25)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.47)
48    448  19918  70662 ( 78.40)     4  0    0   0   0   0     0 (0.00)    0  2543 (3.60)
47    359  20277  70214 ( 77.90)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.62)
46   1270  21547  69855 ( 77.50)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.64)
45   2179  23726  68585 ( 76.09)     1  0    0   0   0   0     0 (0.00)    0  2543 (3.71)
44   2126  25852  66406 ( 73.68)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.83)
43   3926  29778  64280 ( 71.32)     0  0    0   0   0   0     0 (0.00)    0  2543 (3.96)
42   6148  35926  60354 ( 66.96)     1  0    0   0   0   0     0 (0.00)    0  2543 (4.21)
41   1941  37867  54206 ( 60.14)     0  0    0   0   0   0     0 (0.00)    0  2543 (4.69)
40   5024  42891  52265 ( 57.99)     5  0    0   0   0   0     0 (0.00)    0  2543 (4.87)
39    560  43451  47241 ( 52.41)     1  0    0   0   0   0     0 (0.00)    0  2543 (5.38)
38    924  44375  46681 ( 51.79)     0  0    0   0   0   0     0 (0.00)    0  2543 (5.45)
37   2215  46590  45757 ( 50.77)     2  0    0   1   0   0     1 (0.05)    1  2543 (5.56)
36    424  47014  43542 ( 48.31)     0  0    0   0   0   0     0 (0.00)    1  2542 (5.84)
35   3495  50509  43118 ( 47.84)    11  0    0   0   0   0     0 (0.00)    1  2542 (5.90)
34    826  51335  39623 ( 43.96)    11  0    0   0   0   0     0 (0.00)    1  2542 (6.42)
33   1299  52634  38797 ( 43.04)     5  0    0   1   0   0     1 (0.08)    2  2542 (6.55)
32   1191  53825  37498 ( 41.60)    21  0    0   0   0   0     0 (0.00)    2  2541 (6.78)
31    527  54352  36307 ( 40.28)     3  0    0   0   0   0     0 (0.00)    2  2541 (7.00)
30    705  55057  35780 ( 39.70)     3  0    0   0   0   0     0 (0.00)    2  2541 (7.10)
29   1981  57038  35075 ( 38.92)    43  0    0   4   2   0     6 (0.30)    8  2541 (7.24)
28    612  57650  33094 ( 36.72)     7  0    0   1   0   1     2 (0.33)   10  2535 (7.66)
27   1036  58686  32482 ( 36.04)    38  0    0   6   0   0     6 (0.58)   16  2533 (7.80)
26    493  59179  31446 ( 34.89)     9  0    0   0   1   0     1 (0.20)   17  2527 (8.04)
25   1115  60294  30953 ( 34.34)    37  0    0   1   0   0     1 (0.09)   18  2526 (8.16)
24   1052  61346  29838 ( 33.10)    25  0    0   5   3   0     8 (0.76)   26  2525 (8.46)
23    822  62168  28786 ( 31.94)    21  0    0   2   1   0     3 (0.36)   29  2517 (8.74)
22    813  62981  27964 ( 31.03)    30  0    0   9   2   0    11 (1.35)   40  2514 (8.99)
21    993  63974  27151 ( 30.12)    21  0    0   9   1   0    10 (1.01)   50  2503 (9.22)
20    879  64853  26158 ( 29.02)    27  0    0   4   1   1     6 (0.68)   56  2493 (9.53)
19   1413  66266  25279 ( 28.05)    58  0    0  18   8   0    26 (1.84)   82  2487 (9.84)
18    959  67225  23866 ( 26.48)     9  0    0  13   3   0    16 (1.67)   98  2461 (10.31)
17   1017  68242  22907 ( 25.41)    29  0    0  18   3   0    21 (2.06)  119  2445 (10.67)
16   1154  69396  21890 ( 24.29)    46  0    0  25   8   1    34 (2.95)  153  2424 (11.07)
15   1355  70751  20736 ( 23.01)     9  0    0  38   6   1    45 (3.32)  198  2390 (11.53)
14   1304  72055  19381 ( 21.50)    15  0    0  52   6   2    60 (4.60)  258  2345 (12.10)
13   1856  73911  18077 ( 20.06)    26  0    0  95  10   5   110 (5.93)  368  2285 (12.64)
12   1610  75521  16221 ( 18.00)    21  0    0  92  11   4   107 (6.65)  475  2175 (13.41)
11   2620  78141  14611 ( 16.21)    30  0    0 246  23   4   273 (10.42)  748  2068 (14.15)
10   3105  81246  11991 ( 13.30)    57  0    0 354  31  20   405 (13.04)  1153  1795 (14.97)
 9   3993  85239   8886 (  9.86)    81  0    0 466  42  30   538 (13.47)  1691  1390 (15.64)
 8   2238  87477   4893 (  5.43)   107  0    0 253  43  18   314 (14.03)  2005  852 (17.41)
 7   1730  89207   2655 (  2.95)    90  0    0 241  42  14   297 (17.17)  2302  538 (20.26)
 6    824  90031    925 (  1.03)    40  0    0 150  42   7   199 (24.15)  2501  241 (26.05)
 4     77  90108    101 (  0.11)     0  0    0  15   2   0    17 (22.08)  2518   42 (41.58)
 0     24  90132     24 (  0.03)     0  0   24   0   0   1    25 (104.17)  2543   25 (104.17)
-1      0  90132      0 (  0.00)  12895  0    0   0   0   0     0 (0.00)  2543    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  57970  57970  86672 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1730 (2.00)
89    597  58567  28702 ( 33.12)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.03)
88    472  59039  28105 ( 32.43)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.16)
87    514  59553  27633 ( 31.88)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.26)
86    211  59764  27119 ( 31.29)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.38)
85    423  60187  26908 ( 31.05)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.43)
84    399  60586  26485 ( 30.56)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.53)
83    251  60837  26086 ( 30.10)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.63)
82    295  61132  25835 ( 29.81)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.70)
81    592  61724  25540 ( 29.47)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.77)
80     91  61815  24948 ( 28.78)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.93)
79    177  61992  24857 ( 28.68)     0  0    0   0   0   0     0 (0.00)    0  1730 (6.96)
78    185  62177  24680 ( 28.48)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.01)
77    146  62323  24495 ( 28.26)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.06)
76    296  62619  24349 ( 28.09)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.11)
75    133  62752  24053 ( 27.75)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.19)
74     88  62840  23920 ( 27.60)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.23)
73     72  62912  23832 ( 27.50)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.26)
72     67  62979  23760 ( 27.41)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.28)
71     61  63040  23693 ( 27.34)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.30)
70    122  63162  23632 ( 27.27)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.32)
69     72  63234  23510 ( 27.13)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.36)
68     70  63304  23438 ( 27.04)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.38)
67     36  63340  23368 ( 26.96)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.40)
66   4797  68137  23332 ( 26.92)     0  0    0   0   0   0     0 (0.00)    0  1730 (7.41)
65    104  68241  18535 ( 21.39)     0  0    0   0   0   0     0 (0.00)    0  1730 (9.33)
64     31  68272  18431 ( 21.27)     0  0    0   0   0   0     0 (0.00)    0  1730 (9.39)
63      6  68278  18400 ( 21.23)     0  0    0   0   0   0     0 (0.00)    0  1730 (9.40)
62     33  68311  18394 ( 21.22)     0  0    0   0   0   0     0 (0.00)    0  1730 (9.41)
61   1683  69994  18361 ( 21.18)     0  0    0   0   0   0     0 (0.00)    0  1730 (9.42)
60    491  70485  16678 ( 19.24)     0  0    0   0   0   0     0 (0.00)    0  1730 (10.37)
59     55  70540  16187 ( 18.68)     0  0    0   0   0   0     0 (0.00)    0  1730 (10.69)
58     95  70635  16132 ( 18.61)     0  0    0   0   0   0     0 (0.00)    0  1730 (10.72)
57    113  70748  16037 ( 18.50)     0  0    0   0   0   0     0 (0.00)    0  1730 (10.79)
56    363  71111  15924 ( 18.37)     0  0    0   0   0   0     0 (0.00)    0  1730 (10.86)
55    447  71558  15561 ( 17.95)     0  0    0   0   0   0     0 (0.00)    0  1730 (11.12)
54    279  71837  15114 ( 17.44)     0  0    0   0   0   0     0 (0.00)    0  1730 (11.45)
53   1030  72867  14835 ( 17.12)     0  0    0   0   0   0     0 (0.00)    0  1730 (11.66)
52    521  73388  13805 ( 15.93)     0  0    0   0   0   0     0 (0.00)    0  1730 (12.53)
51    344  73732  13284 ( 15.33)     0  0    0   0   0   0     0 (0.00)    0  1730 (13.02)
50    280  74012  12940 ( 14.93)     0  0    0   0   0   0     0 (0.00)    0  1730 (13.37)
49    101  74113  12660 ( 14.61)     0  0    0   0   0   0     0 (0.00)    0  1730 (13.67)
48    152  74265  12559 ( 14.49)     0  0    0   0   0   0     0 (0.00)    0  1730 (13.77)
47    160  74425  12407 ( 14.31)     0  0    0   0   0   0     0 (0.00)    0  1730 (13.94)
46    122  74547  12247 ( 14.13)     0  0    0   0   0   0     0 (0.00)    0  1730 (14.13)
45    150  74697  12125 ( 13.99)     0  0    0   0   0   0     0 (0.00)    0  1730 (14.27)
44    214  74911  11975 ( 13.82)     0  0    0   0   0   0     0 (0.00)    0  1730 (14.45)
43    128  75039  11761 ( 13.57)     0  0    0   0   0   0     0 (0.00)    0  1730 (14.71)
42    149  75188  11633 ( 13.42)     0  0    0   0   0   0     0 (0.00)    0  1730 (14.87)
41    171  75359  11484 ( 13.25)     0  0    0   0   0   0     0 (0.00)    0  1730 (15.06)
40   2343  77702  11313 ( 13.05)     0  0    0   0   0   0     0 (0.00)    0  1730 (15.29)
39     41  77743   8970 ( 10.35)     0  0    0   3   0   0     3 (7.32)    3  1730 (19.29)
38     20  77763   8929 ( 10.30)     0  0    0   0   0   0     0 (0.00)    3  1727 (19.34)
37     27  77790   8909 ( 10.28)     0  0    0   2   0   0     2 (7.41)    5  1727 (19.38)
36     22  77812   8882 ( 10.25)     0  0    0   0   0   0     0 (0.00)    5  1725 (19.42)
35     61  77873   8860 ( 10.22)     0  0    0   0   0   0     0 (0.00)    5  1725 (19.47)
34     71  77944   8799 ( 10.15)     2  0    0   0   0   0     0 (0.00)    5  1725 (19.60)
33     43  77987   8728 ( 10.07)     0  0    0   1   0   0     1 (2.33)    6  1725 (19.76)
32     49  78036   8685 ( 10.02)     0  0    0   2   0   0     2 (4.08)    8  1724 (19.85)
31     28  78064   8636 (  9.96)     0  0    0   0   0   0     0 (0.00)    8  1722 (19.94)
30     42  78106   8608 (  9.93)     0  0    0   1   0   0     1 (2.38)    9  1722 (20.00)
29     98  78204   8566 (  9.88)     0  0    0   3   2   0     5 (5.10)   14  1721 (20.09)
28     40  78244   8468 (  9.77)     1  0    0   1   0   1     2 (5.00)   16  1716 (20.26)
27     70  78314   8428 (  9.72)     5  0    0   6   0   0     6 (8.57)   22  1714 (20.34)
26     54  78368   8358 (  9.64)     1  0    0   4   1   0     5 (9.26)   27  1708 (20.44)
25    353  78721   8304 (  9.58)     3  0    0  24   0   0    24 (6.80)   51  1703 (20.51)
24    112  78833   7951 (  9.17)     6  0    0   7   2   0     9 (8.04)   60  1679 (21.12)
23     90  78923   7839 (  9.04)     2  0    0   5   1   0     6 (6.67)   66  1670 (21.30)
22     80  79003   7749 (  8.94)     2  0    0   8   1   0     9 (11.25)   75  1664 (21.47)
21     92  79095   7669 (  8.85)     0  0    0   4   1   0     5 (5.43)   80  1655 (21.58)
20     87  79182   7577 (  8.74)     4  0    0   3   0   1     4 (4.60)   84  1650 (21.78)
19    218  79400   7490 (  8.64)     6  0    0  12   3   0    15 (6.88)   99  1646 (21.98)
18     88  79488   7272 (  8.39)     1  0    0   8   2   0    10 (11.36)  109  1631 (22.43)
17    153  79641   7184 (  8.29)     3  0    0  13   1   0    14 (9.15)  123  1621 (22.56)
16    252  79893   7031 (  8.11)     3  0    0  17   4   1    22 (8.73)  145  1607 (22.86)
15    283  80176   6779 (  7.82)     2  0    0  37   6   1    44 (15.55)  189  1585 (23.38)
14    281  80457   6496 (  7.49)     0  0    0  30   6   1    37 (13.17)  226  1541 (23.72)
13    522  80979   6215 (  7.17)     0  0    0  69   7   5    81 (15.52)  307  1504 (24.20)
12    417  81396   5693 (  6.57)     3  0    0  64   9   2    75 (17.99)  382  1423 (25.00)
11    819  82215   5276 (  6.09)     5  0    0 143  18   3   164 (20.02)  546  1348 (25.55)
10   1065  83280   4457 (  5.14)     5  0    0 234  22  16   272 (25.54)  818  1184 (26.56)
 9   1514  84794   3392 (  3.91)     3  0    0 294  28  25   347 (22.92)  1165  912 (26.89)
 8    744  85538   1878 (  2.17)     5  0    0 174  25  11   210 (28.23)  1375  565 (30.09)
 7    700  86238   1134 (  1.31)     9  0    0 172  32   9   213 (30.43)  1588  355 (31.31)
 6    391  86629    434 (  0.50)     1  0    0  99  25   5   129 (32.99)  1717  142 (32.72)
 4     36  86665     43 (  0.05)     0  0    0   5   1   0     6 (16.67)  1723   13 (30.23)
 0      7  86672      7 (  0.01)     0  0    7   0   0   0     7 (100.00)  1730    7 (100.00)
-1   3460  90132      0 (  0.00)  13767  0   17 674  94  28   813 (23.50)  2543    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      30       30        1
 35      10       40        3
 39       5       45        4
 40       8       53        6
 41       6       59        8
 42       7       66       11
 43      19       85       16
 45      25      110       18
 46       6      116       19
 47      20      136       29
 48      13      149       36
 49       1      150       36
 50      43      193       49
 51     109      302       66
 52     128      430      101
 53     216      646      135
 54      38      684      146
 55      79      763      153
 56     114      877      131
 57      10      887      130
 58       3      890      130
 59       2      892      132
 60     113     1005      142
 61     315     1320      151
 62       1     1321      152
 63       2     1323      153
 64       3     1326      154
 65       4     1330      156
 66     905     2235       26
 67       7     2242       30
 68      10     2252       33
 69      15     2267       38
 70      20     2287       41
 71       9     2296       44
 72      11     2307       49
 73      14     2321       53
 74      16     2337       50
 75      27     2364       53
 76      42     2406       64
 77      23     2429       68
 78      28     2457       76
 79      29     2486       83
 80      20     2506       86
 81      90     2596       92
 82      43     2639      102
 83      42     2681      102
 84      59     2740      111
 85      68     2808      121
 86      33     2841      129
 87      77     2918      156
 88      66     2984      169
 89      90     3074      187
 90    6742     9816        1

SS region: 2073 (21.12%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  145     -4.0  [-2.2,  0.0]  (2, 0)
 1607     -3.4  [-3.4,  0.0]  (0, 1)
 3397     -3.1  [-3.1,  0.0]  (0, 1)
 4315     -3.3  [-3.3,  0.0]  (0, 1)
 4840     -3.4  [-3.4,  0.0]  (0, 1)
 8245     -3.4  [-3.4,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)   186-  725 [-3.4] (16,1)     ae100109r1         283-823 || local(+/-) (3.5,3.5), distant (0.0,0.0)
LLR breakdown: discreps: -12.6 (<20 part: -12.6 (#=69), >20:0.0 (#=0); in HQ: -5.6, out HQ -7.0), match: 9.2  trail: -0.1  lead: 0.0  total: -3.5 
(0, 0)    57-  959 [-11.7] (0,0)     af090109r1         69-985 || local(+/-) (8.8,7.0), distant (0.0,0.0)
LLR breakdown: discreps: -22.2 (<20 part: -22.2 (#=200), >20:0.0 (#=0); in HQ: -2.2, out HQ -20.0), match: 10.4  lead: 0.0  total: -11.8 
(0, 0)   194-  913 [-5.4] (0,12)     cb100109r1         207-941 || local(+/-) (7.8,11.3), distant (0.0,0.0)
LLR breakdown: discreps: -16.9 (<20 part: -16.9 (#=107), >20:0.0 (#=0); in HQ: 0.0, out HQ -16.9), match: 11.6  trail: -0.2  lead: 0.0  total: -5.5 
(0, 0)   228-  923 [-3.9] (0,0)     df120109r1         244-940 || local(+/-) (8.5,8.3), distant (0.0,0.0)
LLR breakdown: discreps: -17.3 (<20 part: -14.9 (#=69), >20:-2.4 (#=1); in HQ: -6.9, out HQ -10.4), match: 13.3  trail: 0.0  lead: 0.0  total: -4.0 
(0, 0)   215-  653 [-8.0] (0,0)     eb090109r1         225-673 || local(+/-) (9.4,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -12.9 (<20 part: -12.9 (#=124), >20:0.0 (#=0); in HQ: -4.1, out HQ -8.8), match: 4.9  trail: 0.0  lead: 0.0  total: -8.0 
(0, 0)   229-  616 [-5.1] (0,0)     af040109r1         245-634 || local(+/-) (3.9,3.5), distant (0.0,0.0)
LLR breakdown: discreps: -9.4 (<20 part: -9.4 (#=75), >20:0.0 (#=0); in HQ: -4.3, out HQ -5.1), match: 4.3  trail: 0.0  lead: 0.0  total: -5.1 
(0, 0)   206-  760 [-11.4] (0,0)     ff090109r1         215-780 || local(+/-) (6.3,5.0), distant (0.0,0.0)
LLR breakdown: discreps: -20.0 (<20 part: -20.0 (#=145), >20:0.0 (#=0); in HQ: 0.0, out HQ -20.0), match: 8.6  trail: 0.0  lead: 0.0  total: -11.4 
(0, 0)    92-  301 [-7.9] (0,0)     cf080109r1         103-313 || local(+/-) (2.9,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -8.8 (<20 part: -8.8 (#=33), >20:0.0 (#=0); in HQ: -4.5, out HQ -4.3), match: 4.0  trail: 0.0  lead: -3.1  total: -7.9 
(0, 0)   179-  783 [-9.8] (0,0)     ch070109r1         183-792 || local(+/-) (8.6,7.3), distant (0.0,0.0)
LLR breakdown: discreps: -17.1 (<20 part: -15.1 (#=132), >20:-2.0 (#=1); in HQ: 0.0, out HQ -17.1), match: 7.2  trail: 0.0  lead: 0.0  total: -9.9 
(0, 0)   203-  946 [-3.7] (0,0)     ce020109r1         188-934 || local(+/-) (10.9,11.3), distant (0.0,0.0)
LLR breakdown: discreps: -17.2 (<20 part: -17.2 (#=95), >20:0.0 (#=0); in HQ: 0.0, out HQ -17.2), match: 13.4  lead: 0.0  total: -3.8 
(0, 0)   795-  978 [-3.2] (19,0)     ae090109r1         83-266 || local(+/-) (1.7,1.4), distant (0.0,0.0)
LLR breakdown: discreps: -3.0 (<20 part: -3.0 (#=21), >20:0.0 (#=0); in HQ: -1.9, out HQ -1.1), match: 2.7  trail: -3.0  lead: 0.0  total: -3.3 

Gaps in unique-read coverage:  None.

Contig 11.  136 reads; 9949 bp (untrimmed), 9789 (trimmed).  Isolated contig.
      1   940 bb020109f1    853 (  0)  0.86 0.64 0.00    0 (253)    6 ( 10) 
    226  1153 ff010109f1    852 (  0)  0.33 0.00 0.00   28 ( 28)    0 (  0) 
    275  1224 cb010109r1    855 (  0)  0.33 0.00 0.00   52 ( 52)    0 (  0) 
    356  1691 dd040109r1    107 (  0)  2.86 2.86 0.00  186 (186) 1010 (1010) 
    723  1717 ac080109f1    898 (  0)  0.21 0.00 0.00   49 ( 49)    4 (  8) 
    936  1912 ae040109r1    761 (  0)  3.26 0.65 0.11   54 ( 70)    2 ( 68) 
    990  1939 ea030109r1    851 (  0)  0.22 0.22 0.00   52 ( 52)    0 (  0) 
   1155  2090 ea010109r1    858 (  0)  0.00 0.00 0.00   49 ( 49)    0 (  0) 
   1276  2217 ec040109r1    663 (  0)  0.92 1.84 0.00   48 ( 48)  133 (156) 
   1374  2278 fh010109r1    827 (  0)  0.00 0.00 0.00   49 ( 49)    1 (  1) 
C  1393  2372 ae040109f1    862 (  0)  1.37 0.32 0.00    0 (  0)   34 ( 34) 
   1448  2428 df050109r1    816 (  0)  1.50 0.64 0.54   49 ( 49)    1 ( 62) 
   1625  2581 ec010109r1    860 (  0)  0.33 0.11 0.00   53 ( 53)    6 (  6) 
   1674  2602 ba010109f1    801 (  0)  1.37 0.46 0.00   54 ( 54)    0 (  0) 
   1768  2720 cf100109r1    817 (  0)  1.11 1.00 0.00   50 ( 50)    0 ( 44) 
   1855  2793 de010109f1    843 (  0)  1.31 0.22 0.00   25 ( 49)    1 (  1) 
C  1896  2855 bb020109r1    866 (  0)  0.66 0.11 0.00    1 (  6)   47 ( 47) 
   2006  2943 ea040109f1    828 (  0)  1.43 0.33 0.22   28 ( 28)    0 (  0) 
   2026  2962 ed110109r1    863 (  0)  0.00 0.00 0.00   51 ( 51)    1 (  1) 
   2079  3042 df100109r1    809 (  0)  1.37 0.23 0.11   49 ( 49)   40 ( 40) 
   2188  3096 fg040109r1    653 (  0)  3.31 1.02 0.00   20 ( 20)  104 (139) 
   2209  3161 db080109r1    774 (  0)  2.88 0.44 0.33   47 ( 47)    4 ( 61) 
   2226  3192 cf040109f1    892 (  0)  0.43 0.11 0.00   36 ( 36)    0 (  0) 
   2278  3229 ch040109f1    884 (  0)  0.54 0.11 0.00   27 ( 27)    0 (  0) 
C  2395  3367 de030109f1    907 (  0)  0.63 0.00 0.00    0 (  0)   26 ( 26) 
   2432  3381 be070109r1    851 (  0)  0.88 0.11 0.11   46 ( 46)    0 (  0) 
C  2447  3412 ec040109f1    873 (  0)  0.65 0.11 0.11    2 (  2)   41 ( 40) 
   2448  3389 bg070109f1    889 (  0)  0.22 0.00 0.00   27 ( 27)    0 (  0) 
   2488  3462 ad090109r1    870 (  0)  0.11 0.11 0.11   70 ( 70)    0 (  0) 
C  2542  3525 ac080109r1    896 (  0)  0.43 0.00 0.00    0 (  0)   55 ( 55) 
C  2543  3476 ff010109r1    850 (  0)  0.57 0.00 0.00    0 (  0)   50 ( 50) 
   2569  3494 fd110109r1    854 (  0)  0.00 0.00 0.00   47 ( 46)    0 (  0) 
C  2644  3628 dd040109f1    921 (  0)  0.00 0.10 0.00    0 (  0)   28 (  4) 
C  2643  3579 ec010109f1    831 (  0)  1.00 0.22 0.22    1 (  1)   33 ( 33) 
C  2646  3574 ea010109f1    849 (  0)  0.44 0.22 0.11    0 (  0)   29 ( 32) 
C  2678  3633 cb010109f1    864 (  0)  0.86 0.00 0.11    0 ( 21)   30 ( 30) 
C  2723  3626 fh010109f1    837 (  0)  0.00 0.11 0.11    0 (  0)   27 (  3) 
C  2823  3782 ea040109r1    851 (  0)  0.99 0.11 0.00    5 (  5)   47 ( 47) 
   2909  3830 ah120109r1    836 (  0)  0.12 0.00 0.00   57 ( 57)    0 (  0) 
C  2949  3890 dh020109r1    849 (  0)  0.45 0.00 0.00    0 (  4)   50 ( 50) 
   3041  3983 cg020109f1    860 (  0)  0.55 0.00 0.00   28 ( 28)    0 (  0) 
C  3074  4026 be070109f1    871 (  0)  0.11 0.11 0.00    7 (  7)   28 ( 28) 
   3164  4118 ec060109f1    884 (  0)  0.11 0.00 0.00   31 ( 31)    0 (  0) 
   3172  4120 cg100109f1    875 (  0)  0.11 0.11 0.00   31 ( 31)    0 (  0) 
   3403  4337 bd090109f1    876 (  0)  0.00 0.00 0.00   28 ( 28)    0 (  0) 
   3407  4368 ab010109r1    870 (  0)  0.11 0.11 0.00   55 ( 55)    0 (  0) 
C  3469  4411 ba010109r1    747 (  0)  3.48 0.56 0.00    4 ( 64)   48 ( 48) 
C  3465  4392 ed110109f1    571 (  0)  2.95 0.00 0.00  258 (313)   27 ( 27) 
C  3544  4487 bg070109r1    845 (  0)  0.45 0.00 0.11    7 (  7)   45 ( 45) 
   3551  4487 bc020109f1    866 (  0)  0.22 0.22 0.00   28 ( 28)    1 (  1) 
   3620  4556 eh040109f1    873 (  0)  0.22 0.00 0.00   30 ( 30)    0 (  0) 
C  3630  4571 ea030109f1    848 (  0)  1.21 0.11 0.00    0 (  0)   31 ( 31) 
   3721  4665 eh080109f1    741 (  0)  2.86 1.54 0.00   29 ( 29)    6 ( 85) 
C  3790  4756 fg040109f1    786 (  0)  2.78 0.53 0.43    1 ( 42)   31 ( 65) 
   3810  4749 df110109r1    787 (  0)  1.35 1.12 0.00   47 ( 47)    4 ( 77) 
   3864  4796 ec070109f1    859 (  0)  0.44 0.00 0.00   30 ( 30)    3 (  3) 
   3865  4837 eg060109r1    855 (  0)  0.55 0.11 0.22   52 ( 52)   11 ( 11) 
   3882  4825 fa030109r1    854 (  0)  0.45 0.11 0.00   49 ( 60)    0 (  0) 
C  3917  5081 cf040109r1    290 (  0)  8.97 0.92 0.00  671 (679)   59 ( 72) 
C  3919  4849 fd110109f1    875 (  0)  0.11 0.11 0.00    0 (  0)   22 ( 22) 
C  3933  4906 de010109r1    748 (  0)  2.24 1.57 0.00    6 (  6)   77 ( 77) 
C  3956  4915 cf100109f1    889 (  0)  0.54 0.00 0.00    1 (  1)   30 ( 35) 
   3963  4893 db030109r1    557 (  0)  7.20 1.77 0.47   35 ( 76)   49 (244) 
C  4012  4988 ec060109r1    834 (  0)  1.73 0.32 0.22    0 ( 51)   51 ( 51) 
   4066  5046 dd060109f1    819 (  0)  6.09 0.00 0.00   29 (152)    0 (  0) 
C  4109  5035 ah120109f1    856 (  0)  0.11 0.22 0.00    0 (  0)   34 ( 34) 
C  4307  5283 ch040109r1    684 (  0)  3.95 0.60 0.00   79 (202)   63 ( 77) 
C  4349  5300 bd090109r1    861 (  0)  0.11 0.00 0.00    1 (  1)   51 ( 51) 
   4366  5352 ab040109r1    885 (  0)  0.22 0.00 0.00   65 ( 65)    0 (  0) 
C  4387  5339 ab010109f1    827 (  0)  0.98 0.33 0.33    0 (  8)   36 ( 46) 
C  4474  5458 ad090109f1    896 (  0)  0.11 0.00 0.00    0 (  0)   54 ( 54) 
C  4651  5603 bc020109r1    815 (  0)  2.00 0.00 0.11    1 ( 33)   50 ( 50) 
C  4803  5751 cg100109r1    799 (  0)  1.56 1.00 0.00    0 ( 57)   50 ( 50) 
C  4848  5805 eh080109r1    859 (  0)  0.55 0.11 0.00    5 (  5)   50 ( 50) 
   4881  5831 ag020109f1    849 (  0)  0.88 0.33 0.00   36 ( 36)    6 (  6) 
C  4882  5827 ec070109r1    845 (  0)  0.67 0.00 0.22    0 ( 29)   49 ( 49) 
C  4998  5946 df110109f1    773 (  0)  0.62 0.00 0.00    0 (  0)  143 (162) 
C  5034  5984 fa030109f1    886 (  0)  0.22 0.00 0.11    3 (  3)   28 ( 28) 
C  5427  6418 dd060109r1    895 (  0)  0.63 0.11 0.00    0 ( 10)   47 ( 47) 
   5449  6406 ah040109r1    866 (  0)  0.44 0.00 0.00   54 ( 54)    1 (  1) 
C  5527  6482 eh040109r1    877 (  0)  0.11 0.00 0.00    0 (  0)   48 ( 48) 
   5699  6631 ah110109r1    837 (  0)  0.45 0.23 0.00   48 ( 52)    4 (  4) 
   5858  6815 eh050109r1    872 (  0)  0.11 0.11 0.11   50 ( 50)    1 (  1) 
C  5886  6838 eg060109f1    796 (  0)  2.28 0.22 0.76    0 (106)   30 ( 30) 
   5986  6966 fd060109r1    785 (  0)  3.11 0.64 0.21   48 ( 12)    2 ( 40) 
   5986  6963 ed060109r1    882 (  0)  0.75 0.00 0.11   48 ( 11)    0 (  0) 
   6057  7032 fe060109f1    910 (  0)  0.32 0.00 0.11   30 ( 30)    0 (  0) 
   6140  7075 fc110109r1    853 (  0)  0.45 0.00 0.00   52 (  8)    0 (  0) 
   6143  7067 ec120109r1    849 (  0)  0.11 0.00 0.00   49 (  7)    6 (  6) 
   6205  7138 ea080109f1    876 (  0)  0.22 0.00 0.00   31 ( 31)    1 (  1) 
   6228  7179 ch090109f1    881 (  0)  0.65 0.11 0.00   29 ( 29)    0 (  9) 
   6268  7213 cd100109f1    888 (  0)  0.22 0.11 0.11   23 ( 23)    0 (  0) 
   6322  7269 bg050109f1    889 (  0)  0.44 0.00 0.00   29 ( 29)    0 (  0) 
   6357  7313 ec080109r1    817 (  0)  1.45 0.56 0.00   49 ( 49)   14 ( 63) 
   6412  7358 ah100109f1    868 (  0)  0.88 0.11 0.00   35 ( 35)    1 (  1) 
   6438  7408 ad080109f1    892 (  0)  0.53 0.00 0.42   27 ( 27)    0 (  0) 
   6467  7371 bc120109f1    846 (  0)  0.23 0.11 0.00   34 ( 34)    0 (  0) 
C  6617  7568 ag020109r1    842 (  0)  1.23 0.11 0.11    0 ( 14)   57 ( 57) 
   6629  7582 cb090109r1    701 (  0)  5.06 0.56 0.45   64 ( 64)    1 ( 95) 
   6731  7659 cg110109f1    874 (  0)  0.44 0.00 0.11   29 ( 29)    0 (  0) 
   6774  7698 bg090109r1    783 (  0)  1.30 0.12 0.36   50 ( 50)   31 ( 31) 
   6773  7688 ea110109f1    851 (  0)  0.45 0.22 0.22   26 ( 26)    0 (  0) 
   6995  7914 bh100109f1    881 (  0)  0.00 0.00 0.00   29 ( 29)    0 (  0) 
   7032  7966 ae120109r1    867 (  0)  0.11 0.00 0.00   55 ( 15)    0 (  0) 
C  7038  8000 ah040109f1    898 (  0)  0.54 0.00 0.00    0 (  0)   38 ( 38) 
   7041  7967 bb120109r1    863 (  0)  0.23 0.00 0.00   49 (  8)    0 (  0) 
C  7128  8096 ab040109f1    925 (  0)  0.21 0.00 0.00    0 (  0)   26 ( 26) 
C  7176  8113 ah110109f1    874 (  0)  0.33 0.11 0.11    0 (  0)   35 ( 35) 
C  7231  8217 fd060109f1    920 (  0)  0.31 0.10 0.21    0 (  0)   30 ( 17) 
   7251  8210 ag030109r1    872 (  0)  0.55 0.00 0.00   54 ( 54)    4 (  4) 
C  7257  8208 ea080109r1    859 (  0)  0.67 0.11 0.00    0 ( 25)   58 ( 58) 
C  7262  8214 ed060109f1    860 (  0)  0.97 0.32 0.22    2 (  2)   27 ( 14) 
C  7327  8295 bg050109r1    876 (  0)  0.54 0.11 0.11    0 ( 16)   51 ( 51) 
   7352  8308 ac020109r1    876 (  0)  0.22 0.00 0.00   54 ( 21)    0 (  0) 
   7355  8301 cf020109r1    779 (  0)  2.23 1.00 0.00   50 ( 17)    0 ( 91) 
C  7492  8455 cd100109r1    722 (  0)  2.71 0.59 0.12   62 ( 62)   53 ( 63) 
C  7495  8419 bc120109r1    837 (  0)  0.23 0.11 0.00    0 (  0)   50 ( 50) 
C  7623  8587 dg040109r1    851 (  0)  0.33 0.11 0.00    0 (  0)   56 ( 56) 
C  7653  8628 fe060109r1    872 (  0)  0.11 0.00 0.00    0 (  0)   49 ( 49) 
C  7662  8597 fc110109f1    845 (  0)  0.11 0.00 0.22    0 (  0)   28 (  0) 
C  7690  8598 ec120109f1    816 (  0)  0.23 0.00 0.23    0 (  0)   29 (  0) 
C  7739  8674 ea110109r1    828 (  0)  0.00 0.11 0.00    1 (  1)   49 ( 49) 
C  7782  8721 bh100109r1    814 (  0)  0.23 0.00 0.00    0 (  0)   63 ( 63) 
C  7821  8799 ad080109r1    856 (  0)  0.22 0.00 0.00    1 (  1)   52 ( 52) 
C  7842  8798 eh050109f1    698 (  0)  2.23 0.82 0.00   76 (110)   28 ( 28) 
C  7958  8883 cg110109r1    794 (  0)  0.46 0.00 0.00    1 (  1)   50 ( 50) 
C  8090  9041 ch090109r1    654 (  0)  3.91 0.80 0.23   30 ( 71)   52 ( 83) 
C  8128  9083 cb090109f1    825 (  0)  1.08 0.00 0.11    0 ( 16)   31 ( 31) 
C  8159  9110 ec080109f1    828 (  0)  0.11 0.54 0.00    1 (  1)   28 ( 28) 
C  8347  9298 ag030109f1    809 (  0)  0.76 0.11 0.11    1 (  1)   30 ( 30) 
C  8588  9540 ah100109r1    818 (  0)  0.22 0.11 0.00    1 (  1)   56 ( 56) 
C  8666  9621 ac020109f1    843 (  0)  0.00 0.22 0.22    0 (  0)   27 ( 27) 
C  8669  9619 cf020109f1    713 (  0)  2.81 1.08 0.65    0 ( 90)   27 ( 63) 
C  8916  9854 bg090109f1    815 (  0)  0.11 0.00 0.00    0 (  0)   28 ( 28) 
C  8955  9864 bb120109f1    778 (  0)  0.23 0.00 0.00    0 (  0)   28 ( 28) 
C  9013  9949 ae120109f1    832 (  0)  0.21 0.00 0.00    0 ( 10)    0 (113) 

Overall discrep rates (%):             0.95 0.23 0.08

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    6447  64.8    6447  64.8    0.00
 89      14   0.1    6461  64.9    0.00
 88      29   0.3    6490  65.2    0.00
 87      19   0.2    6509  65.4    0.00
 86      24   0.2    6533  65.7    0.00
 85      25   0.3    6558  65.9    0.00
 84      15   0.2    6573  66.1    0.00
 83      13   0.1    6586  66.2    0.00
 82      18   0.2    6604  66.4    0.00
 81      50   0.5    6654  66.9    0.00
 80      12   0.1    6666  67.0    0.00
 79      13   0.1    6679  67.1    0.00
 78       4   0.0    6683  67.2    0.00
 77      10   0.1    6693  67.3    0.00
 76      31   0.3    6724  67.6    0.00
 75      21   0.2    6745  67.8    0.00
 74       7   0.1    6752  67.9    0.00
 73       5   0.1    6757  67.9    0.00
 72       6   0.1    6763  68.0    0.00
 71       5   0.1    6768  68.0    0.00
 70      13   0.1    6781  68.2    0.00
 69       6   0.1    6787  68.2    0.00
 68       4   0.0    6791  68.3    0.00
 66    1347  13.5    8138  81.8    0.00
 65       1   0.0    8139  81.8    0.00
 64       1   0.0    8140  81.8    0.00
 63       1   0.0    8141  81.8    0.00
 62       1   0.0    8142  81.8    0.00
 61     708   7.1    8850  89.0    0.00
 60      61   0.6    8911  89.6    0.00
 59       2   0.0    8913  89.6    0.00
 57       7   0.1    8920  89.7    0.00
 56      59   0.6    8979  90.3    0.00
 55     160   1.6    9139  91.9    0.00
 54      23   0.2    9162  92.1    0.00
 53     208   2.1    9370  94.2    0.00
 52      74   0.7    9444  94.9    0.00
 51      94   0.9    9538  95.9    0.00
 50      40   0.4    9578  96.3    0.00
 49       2   0.0    9580  96.3    0.00
 48       4   0.0    9584  96.3    0.00
 47      19   0.2    9603  96.5    0.00
 46       3   0.0    9606  96.6    0.00
 45       9   0.1    9615  96.6    0.01
 44      12   0.1    9627  96.8    0.01
 43      10   0.1    9637  96.9    0.01
 42      41   0.4    9678  97.3    0.01
 41       8   0.1    9686  97.4    0.01
 40      40   0.4    9726  97.8    0.01
 39       4   0.0    9730  97.8    0.01
 38       6   0.1    9736  97.9    0.01
 37      11   0.1    9747  98.0    0.02
 36       2   0.0    9749  98.0    0.02
 35      22   0.2    9771  98.2    0.02
 34       1   0.0    9772  98.2    0.02
 32       1   0.0    9773  98.2    0.03
 31       1   0.0    9774  98.2    0.03
 29       8   0.1    9782  98.3    0.04
 27       4   0.0    9786  98.4    0.04
 22       3   0.0    9789  98.4    0.06
 -1     160   1.6    9949 100.0  160.06   (quality -1 = terminal quality 0)

Avg. full length: 9949.0, trimmed (qual > -1): 9789.0
Avg. quality: 79.2 per base

Initial, terminal qual 0 segments:  1-80, 9870-9949

Regions of LLR- adjusted quality < 2.0:
1-80, 9870-9949, 

2 regions, avg size 80.0, avg spacing 4974.5

First_start: 254, last_end: 9836

Slack, # used pairs (max_score), unused
 0  1054  (19.9)     0 ( 0.0)     1697
 1   538  (19.8)     0 ( 0.0)       63
 2   110  (19.8)     0 ( 0.0)        0
 3    35  (17.8)     0 ( 0.0)        0
 4    10  (19.1)     0 ( 0.0)        0
 5     8  (13.4)     0 ( 0.0)        0
 6     1  ( 3.7)     0 ( 0.0)        0
 7     2  (17.0)     0 ( 0.0)        0
 8     1  (11.2)     0 ( 0.0)        0
10     1  (13.8)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 8309 - right     1641+      cf020109r1   (7355)    No           2594+

Bottom strand: 
 left -  1392     1392+      ae040109f1   (2372)    No           2372+
 9950 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  18290  18290 121389 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.24)
51  10943  29233 103099 ( 84.93)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.46)
50   3454  32687  92156 ( 75.92)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.64)
48    619  33306  88702 ( 73.07)     1  0    0   0   0   0     0 (0.00)    0  1509 (1.70)
47    489  33795  88083 ( 72.56)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.71)
46   2287  36082  87594 ( 72.16)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.72)
45   3991  40073  85307 ( 70.28)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.77)
44   2936  43009  81316 ( 66.99)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.86)
43   5883  48892  78380 ( 64.57)     0  0    0   0   0   0     0 (0.00)    0  1509 (1.93)
42   8337  57229  72497 ( 59.72)     0  0    0   0   0   0     0 (0.00)    0  1509 (2.08)
41   2253  59482  64160 ( 52.85)     0  0    0   0   0   0     0 (0.00)    0  1509 (2.35)
40   8043  67525  61907 ( 51.00)     6  0    0   0   0   0     0 (0.00)    0  1509 (2.44)
39    730  68255  53864 ( 44.37)     1  0    0   0   0   0     0 (0.00)    0  1509 (2.80)
38   1130  69385  53134 ( 43.77)     0  0    0   0   0   0     0 (0.00)    0  1509 (2.84)
37   3135  72520  52004 ( 42.84)     5  0    0   0   0   0     0 (0.00)    0  1509 (2.90)
36    439  72959  48869 ( 40.26)     3  0    0   0   0   0     0 (0.00)    0  1509 (3.09)
35   4493  77452  48430 ( 39.90)    19  0    0   0   0   0     0 (0.00)    0  1509 (3.12)
34   1095  78547  43937 ( 36.20)    22  0    0   0   0   0     0 (0.00)    0  1509 (3.43)
33   1513  80060  42842 ( 35.29)     3  0    0   0   0   0     0 (0.00)    0  1509 (3.52)
32   1749  81809  41329 ( 34.05)    24  0    0   0   0   0     0 (0.00)    0  1509 (3.65)
31    608  82417  39580 ( 32.61)     5  0    0   0   0   0     0 (0.00)    0  1509 (3.81)
30    822  83239  38972 ( 32.11)     8  0    0   0   1   0     1 (0.12)    1  1509 (3.87)
29   3033  86272  38150 ( 31.43)    86  0    0   1   0   0     1 (0.03)    2  1508 (3.95)
28    820  87092  35117 ( 28.93)    16  0    0   1   0   0     1 (0.12)    3  1507 (4.29)
27   1233  88325  34297 ( 28.25)    47  0    0   0   1   0     1 (0.08)    4  1506 (4.39)
26    604  88929  33064 ( 27.24)    30  0    0   1   0   0     1 (0.17)    5  1505 (4.55)
25   1724  90653  32460 ( 26.74)    59  0    0   0   1   0     1 (0.06)    6  1504 (4.63)
24   1330  91983  30736 ( 25.32)    36  0    0   2   2   0     4 (0.30)   10  1503 (4.89)
23   1022  93005  29406 ( 24.22)    38  0    0   1   2   0     3 (0.29)   13  1499 (5.10)
22    962  93967  28384 ( 23.38)    62  0    0   3   1   0     4 (0.42)   17  1496 (5.27)
21   1237  95204  27422 ( 22.59)    14  0    0   4   1   0     5 (0.40)   22  1492 (5.44)
20   1110  96314  26185 ( 21.57)    43  0    0   1   1   0     2 (0.18)   24  1487 (5.68)
19   1627  97941  25075 ( 20.66)   104  0    0   2   2   0     4 (0.25)   28  1485 (5.92)
18   1109  99050  23448 ( 19.32)    26  0    0   6   1   0     7 (0.63)   35  1481 (6.32)
17   1144 100194  22339 ( 18.40)    33  0    0   6   4   1    11 (0.96)   46  1474 (6.60)
16   1212 101406  21195 ( 17.46)    97  0    0   4   6   1    11 (0.91)   57  1463 (6.90)
15   1469 102875  19983 ( 16.46)    48  0    0   8   3   1    12 (0.82)   69  1452 (7.27)
14   1232 104107  18514 ( 15.25)    32  0    0  19  11   2    32 (2.60)  101  1440 (7.78)
13   1623 105730  17282 ( 14.24)    60  0    0  33   7   4    44 (2.71)  145  1408 (8.15)
12   1697 107427  15659 ( 12.90)    28  0    0  39  13   6    58 (3.42)  203  1364 (8.71)
11   2107 109534  13962 ( 11.50)    50  0    0  69  28   9   106 (5.03)  309  1306 (9.35)
10   2760 112294  11855 (  9.77)    75  0    0 110  22  12   144 (5.22)  453  1200 (10.12)
 9   3793 116087   9095 (  7.49)   190  0    0 230  47  34   311 (8.20)  764  1056 (11.61)
 8   2361 118448   5302 (  4.37)   138  0    0 190  41   9   240 (10.17)  1004  745 (14.05)
 7   2013 120461   2941 (  2.42)    75  0    0 244  36   8   288 (14.31)  1292  505 (17.17)
 6    800 121261    928 (  0.76)    42  0    0 122  37   4   163 (20.38)  1455  217 (23.38)
 4     81 121342    128 (  0.11)    18  0    0   5   2   0     7 (8.64)  1462   54 (42.19)
 0     47 121389     47 (  0.04)     1  0   46   0   1   0    47 (100.00)  1509   47 (100.00)
-1     71 121460      0 (  0.00)  6960  0    0   0   0   0     0 (0.00)  1509    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  88899  88899 119132 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1022 (0.86)
89    185  89084  30233 ( 25.38)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.38)
88    332  89416  30048 ( 25.22)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.40)
87    246  89662  29716 ( 24.94)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.44)
86    298  89960  29470 ( 24.74)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.47)
85    277  90237  29172 ( 24.49)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.50)
84    172  90409  28895 ( 24.25)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.54)
83    180  90589  28723 ( 24.11)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.56)
82    237  90826  28543 ( 23.96)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.58)
81    561  91387  28306 ( 23.76)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.61)
80    112  91499  27745 ( 23.29)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.68)
79     56  91555  27633 ( 23.20)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.70)
78     23  91578  27577 ( 23.15)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.71)
77     45  91623  27554 ( 23.13)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.71)
76    238  91861  27509 ( 23.09)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.72)
75     69  91930  27271 ( 22.89)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.75)
74     34  91964  27202 ( 22.83)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.76)
73     18  91982  27168 ( 22.80)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.76)
72     43  92025  27150 ( 22.79)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.76)
71     36  92061  27107 ( 22.75)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.77)
70    109  92170  27071 ( 22.72)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.78)
69     21  92191  26962 ( 22.63)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.79)
68     31  92222  26941 ( 22.61)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.79)
67     11  92233  26910 ( 22.59)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.80)
66   9134 101367  26899 ( 22.58)     0  0    0   0   0   0     0 (0.00)    0  1022 (3.80)
65     72 101439  17765 ( 14.91)     0  0    0   0   0   0     0 (0.00)    0  1022 (5.75)
64     16 101455  17693 ( 14.85)     0  0    0   0   0   0     0 (0.00)    0  1022 (5.78)
63      9 101464  17677 ( 14.84)     0  0    0   0   0   0     0 (0.00)    0  1022 (5.78)
62     18 101482  17668 ( 14.83)     0  0    0   0   0   0     0 (0.00)    0  1022 (5.78)
61   4294 105776  17650 ( 14.82)     0  0    0   0   0   0     0 (0.00)    0  1022 (5.79)
60    247 106023  13356 ( 11.21)     0  0    0   0   0   0     0 (0.00)    0  1022 (7.65)
59     49 106072  13109 ( 11.00)     0  0    0   0   0   0     0 (0.00)    0  1022 (7.80)
58     31 106103  13060 ( 10.96)     0  0    0   0   0   0     0 (0.00)    0  1022 (7.83)
57     67 106170  13029 ( 10.94)     0  0    0   0   0   0     0 (0.00)    0  1022 (7.84)
56    287 106457  12962 ( 10.88)     0  0    0   0   0   0     0 (0.00)    0  1022 (7.88)
55    912 107369  12675 ( 10.64)     0  0    0   0   0   0     0 (0.00)    0  1022 (8.06)
54    228 107597  11763 (  9.87)     0  0    0   0   0   0     0 (0.00)    0  1022 (8.69)
53   1075 108672  11535 (  9.68)     0  0    0   0   0   0     0 (0.00)    0  1022 (8.86)
52    292 108964  10460 (  8.78)     0  0    0   0   0   0     0 (0.00)    0  1022 (9.77)
51    329 109293  10168 (  8.54)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.05)
50    178 109471   9839 (  8.26)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.39)
49     83 109554   9661 (  8.11)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.58)
48     75 109629   9578 (  8.04)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.67)
47    108 109737   9503 (  7.98)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.75)
46     72 109809   9395 (  7.89)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.88)
45    114 109923   9323 (  7.83)     0  0    0   0   0   0     0 (0.00)    0  1022 (10.96)
44    156 110079   9209 (  7.73)     0  0    0   0   0   0     0 (0.00)    0  1022 (11.10)
43     59 110138   9053 (  7.60)     0  0    0   0   0   0     0 (0.00)    0  1022 (11.29)
42    154 110292   8994 (  7.55)     0  0    0   0   0   0     0 (0.00)    0  1022 (11.36)
41    162 110454   8840 (  7.42)     0  0    0   0   0   0     0 (0.00)    0  1022 (11.56)
40   2255 112709   8678 (  7.28)     0  0    0   0   0   0     0 (0.00)    0  1022 (11.78)
39     56 112765   6423 (  5.39)     0  0    0   0   0   0     0 (0.00)    0  1022 (15.91)
38     20 112785   6367 (  5.34)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.05)
37     27 112812   6347 (  5.33)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.10)
36     25 112837   6320 (  5.31)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.17)
35     46 112883   6295 (  5.28)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.24)
34     37 112920   6249 (  5.25)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.35)
33     30 112950   6212 (  5.21)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.45)
32     48 112998   6182 (  5.19)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.53)
31     24 113022   6134 (  5.15)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.66)
30     23 113045   6110 (  5.13)     0  0    0   0   0   0     0 (0.00)    0  1022 (16.73)
29    117 113162   6087 (  5.11)     1  0    0   1   0   0     1 (0.85)    1  1022 (16.79)
28     24 113186   5970 (  5.01)     0  0    0   1   0   0     1 (4.17)    2  1021 (17.10)
27     71 113257   5946 (  4.99)     0  0    0   2   1   2     5 (7.04)    7  1020 (17.15)
26     51 113308   5875 (  4.93)     0  0    0   1   0   0     1 (1.96)    8  1015 (17.28)
25    299 113607   5824 (  4.89)     0  0    0   0   2   0     2 (0.67)   10  1014 (17.41)
24     77 113684   5525 (  4.64)     0  0    0   1   1   0     2 (2.60)   12  1012 (18.32)
23     48 113732   5448 (  4.57)     0  0    0   1   2   0     3 (6.25)   15  1010 (18.54)
22     45 113777   5400 (  4.53)     0  0    0   3   1   0     4 (8.89)   19  1007 (18.65)
21     56 113833   5355 (  4.50)     0  0    0   5   1   0     6 (10.71)   25  1003 (18.73)
20     89 113922   5299 (  4.45)     0  0    0   1   1   0     2 (2.25)   27  997 (18.81)
19    149 114071   5210 (  4.37)     0  0    0   1   1   0     2 (1.34)   29  995 (19.10)
18     67 114138   5061 (  4.25)     0  0    0   6   0   0     6 (8.96)   35  993 (19.62)
17    101 114239   4994 (  4.19)     0  0    0   3   4   0     7 (6.93)   42  987 (19.76)
16    157 114396   4893 (  4.11)     0  0    0   3   4   1     8 (5.10)   50  980 (20.03)
15    122 114518   4736 (  3.98)     0  0    0   6   2   3    11 (9.02)   61  972 (20.52)
14    166 114684   4614 (  3.87)     0  0    0  15   7   1    23 (13.86)   84  961 (20.83)
13    296 114980   4448 (  3.73)     0  0    0  17   7   4    28 (9.46)  112  938 (21.09)
12    278 115258   4152 (  3.49)     0  0    0  24   9   4    37 (13.31)  149  910 (21.92)
11    441 115699   3874 (  3.25)     0  0    0  44  20   8    72 (16.33)  221  873 (22.53)
10    580 116279   3433 (  2.88)     1  0    0  71  15   6    92 (15.86)  313  801 (23.33)
 9   1036 117315   2853 (  2.39)     1  0    0 142  23  19   184 (17.76)  497  709 (24.85)
 8    650 117965   1817 (  1.53)     0  0    0 130  30   3   163 (25.08)  660  525 (28.89)
 7    753 118718   1167 (  0.98)     0  0    0 189  31   8   228 (30.28)  888  362 (31.02)
 6    364 119082    414 (  0.35)     0  0    0  87  30   3   120 (32.97)  1008  134 (32.37)
 4     38 119120     50 (  0.04)     0  0    0   1   1   0     2 (5.26)  1010   14 (28.00)
 0     12 119132     12 (  0.01)     0  0   11   0   1   0    12 (100.00)  1022   12 (100.00)
-1   2328 121460      0 (  0.00)  8502  0   35 346  77  29   487 (20.92)  1509    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     160      160        2
 22       3      163        3
 27       4      167        4
 29       8      175        7
 31       1      176        8
 32       1      177        8
 34       1      178        7
 35      22      200       11
 36       2      202       11
 37      11      213       12
 38       6      219       14
 39       4      223       15
 40      40      263       17
 41       8      271       18
 42      41      312       20
 43      10      322       21
 44      12      334       19
 45       9      343       18
 46       3      346       16
 47      19      365       19
 48       4      369       19
 49       2      371       20
 50      40      411       26
 51      94      505       44
 52      74      579       59
 53     208      787       94
 54      23      810      100
 55     160      970      134
 56      59     1029      125
 57       7     1036      124
 59       2     1038      125
 60      61     1099      125
 61     708     1807      183
 62       1     1808      184
 63       1     1809      185
 64       1     1810      185
 65       1     1811      186
 66    1347     3158        9
 68       4     3162       12
 69       6     3168       13
 70      13     3181       17
 71       5     3186       19
 72       6     3192       21
 73       5     3197       23
 74       7     3204       26
 75      21     3225       24
 76      31     3256       33
 77      10     3266       32
 78       4     3270       33
 79      13     3283       32
 80      12     3295       30
 81      50     3345       35
 82      18     3363       41
 83      13     3376       42
 84      15     3391       45
 85      25     3416       41
 86      24     3440       39
 87      19     3459       42
 88      29     3488       50
 89      14     3502       53
 90    6447     9949        1

SS region: 3033 (30.49%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 2305     -3.7  [-2.0,  0.0]  (1, 1)
 3601     -3.4  [-3.4,  0.0]  (0, 1)
 4699     -3.0  [-3.0,  0.0]  (1, 0)
 6915     -3.8  [-2.1,  0.0]  (2, 0)
 8188     -5.8  [-2.9,  0.0]  (0, 2)
 8570     -6.3  [-3.4,  0.0]  (0, 2)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem: None.

Gaps in unique-read coverage:  None.

Contig 12.  145 reads; 9829 bp (untrimmed), 9674 (trimmed).
      1   960 bc070109r1    879 (  0)  0.42 0.00 0.10    0 ( 75)    0 (  4) 
     25   971 fd010109r1    810 (  0)  0.22 0.00 0.11   51 ( 51)    3 (  3) 
    133  1102 fb030109f1    877 (  0)  0.00 0.11 0.00   26 ( 26)    0 (  0) 
    145  1088 fe010109f1    854 (  0)  0.00 0.00 0.00   28 ( 28)    1 (  1) 
    585  1510 cc120109f1    814 (  0)  0.46 0.00 0.00   53 ( 53)    0 (  0) 
    676  1566 df020109r1    553 (  0)  2.69 0.75 0.00   26 ( 26)  197 (286) 
    855  1817 dd050109f1    220 (  0)  16.87 0.80 0.00  121 (154)   95 (514) 
    884  1856 ab080109r1    849 (  0)  0.22 0.11 0.11   52 ( 52)    0 (  0) 
   1010  1969 fe090109f1    857 (  0)  0.00 0.00 0.11   28 ( 28)    0 (  0) 
   1141  2094 fd090109f1    845 (  0)  0.54 0.00 0.00   28 ( 28)    4 (  4) 
   1145  2115 df070109r1    801 (  0)  0.98 0.55 0.11   48 ( 59)    7 (  7) 
   1158  2126 ab020109f1    866 (  0)  0.11 0.00 0.00   35 ( 35)    1 (  1) 
   1192  2110 eb120109f1     41 (  0)  0.00 0.00 0.00   35 ( 35)  840 (840) 
   1430  2378 be030109f1    845 (  0)  0.00 0.00 0.00   31 ( 31)    1 (  1) 
   1588  2553 fc050109r1    862 (  0)  0.00 0.11 0.00   49 ( 49)    0 (  0) 
   1690  2639 bb050109f1    827 (  0)  1.20 0.11 0.11   30 ( 30)    3 ( 32) 
C  1770  2707 fe010109r1    819 (  0)  0.45 0.00 0.11    0 (  0)   49 ( 49) 
C  1791  2757 fb030109r1    861 (  0)  0.00 0.00 0.00    0 (  0)   49 ( 49) 
   1800  2741 fa100109r1    805 (  0)  0.57 0.00 0.00   60 ( 60)    0 (  0) 
   1806  2731 cb120109r1    805 (  0)  0.46 0.00 0.00   50 ( 50)    0 (  0) 
   1887  2850 fb050109r1    816 (  0)  0.88 0.22 0.22   47 ( 47)    6 (  6) 
C  2054  2980 cc120109r1    707 (  0)  3.33 0.36 0.00   32 ( 32)   55 ( 59) 
C  2092  3038 fd010109f1    850 (  0)  0.43 0.11 0.11    0 (  0)   26 ( 26) 
C  2095  3031 bc070109f1    857 (  0)  0.11 0.00 0.00    0 (  0)   26 ( 26) 
   2100  3043 af110109f1    853 (  0)  0.22 0.00 0.00   35 ( 34)    0 (  0) 
C  2215  3172 dd050109r1    552 (  0)  3.97 1.56 0.00  241 (343)   12 ( 12) 
   2279  3239 cc070109f1    837 (  0)  1.18 0.32 0.22   29 ( 29)    2 ( 24) 
   2287  3248 cc040109r1    610 (  0)  6.12 0.58 1.15   44 ( 44)   52 (248) 
C  2318  3273 fd090109r1    852 (  0)  0.44 0.00 0.00    5 (  5)   50 ( 50) 
C  2526  3515 ab080109f1    863 (  0)  0.11 0.11 0.00    1 (  1)   50 ( 50) 
   2530  3443 ef110109f1    770 (  0)  1.01 0.34 0.23   27 ( 27)    0 (  0) 
   2559  3506 fe020109f1    836 (  0)  0.00 0.00 0.00   30 ( 30)    0 (  0) 
   2643  3618 af070109r1    824 (  0)  0.22 0.00 0.11   56 ( 56)    0 (  0) 
C  2661  3647 ab020109r1    802 (  0)  0.33 0.55 0.00    0 (  4)   73 ( 73) 
C  2736  3701 be030109r1    825 (  0)  0.22 0.11 0.00    0 (  0)   51 ( 51) 
C  2899  3853 fe090109r1    783 (  0)  0.66 0.00 0.00    0 (  0)   51 ( 50) 
C  2899  3865 bb050109r1    800 (  0)  0.33 0.00 0.11    0 (  0)   51 ( 51) 
   2902  3848 ec090109f1    800 (  0)  0.22 0.00 0.00   29 ( 29)    1 (  1) 
   3026  3976 bd080109f1    806 (  0)  0.43 0.00 0.11   24 ( 28)    1 (  1) 
   3161  4130 cd070109f1    769 (  0)  1.27 0.21 0.21   28 ( 28)    0 (  0) 
C  3167  4101 fa100109f1    744 (  0)  1.00 0.11 0.11    2 (  2)   29 ( 29) 
C  3167  4138 fc050109f1    803 (  0)  0.32 0.11 0.00    0 (  0)   32 ( 32) 
C  3342  4311 fb050109f1    829 (  0)  0.00 0.00 0.00    0 (  0)   28 ( 28) 
   3360  4337 af060109f1    802 (  0)  0.53 0.42 0.00   34 ( 34)    0 (  0) 
C  3362  4302 af110109r1    774 (  0)  0.00 0.23 0.00    0 (  0)   54 ( 54) 
C  3386  4321 bf090109r1    754 (  0)  0.79 0.11 0.00    0 (  0)   50 ( 50) 
   3401  4360 cd030109f1    819 (  0)  0.11 0.00 0.11   26 ( 26)    0 (  0) 
C  3414  4340 cb120109f1    779 (  0)  0.33 0.00 0.11    0 (  0)   28 ( 28) 
   3429  4388 cd020109r1    796 (  0)  0.44 0.00 0.11   50 ( 50)    0 ( 10) 
C  3454  4493 cc070109r1    364 (  0)  4.84 3.11 0.17  422 (504)   39 ( 56) 
C  3456  4414 dc040109f1    282 (  0)  23.23 0.12 0.24    4 (262)  124 (349) 
   3504  4462 da080109r1    799 (  0)  0.77 0.00 0.00   47 ( 47)    1 ( 17) 
C  3524  4493 af070109f1    831 (  0)  0.21 0.00 0.00    0 (  0)   36 ( 36) 
   3563  4553 db060109r1    822 (  0)  0.65 0.11 0.00   61 ( 61)    0 (  0) 
   3566  4525 ed020109r1    805 (  0)  0.44 0.11 0.00   49 ( 49)    0 ( 17) 
C  3616  4558 fe020109r1    801 (  0)  0.22 0.00 0.00    0 (  0)   50 ( 61) 
   3662  4642 ed050109r1    833 (  0)  0.86 0.00 0.00   47 ( 47)    7 ( 11) 
   3678  4655 de060109f1    810 (  0)  1.60 0.21 0.11   30 ( 96)   10 ( 10) 
   3714  4692 de070109f1    716 (  0)  4.00 1.05 0.42   28 ( 64)    0 (  0) 
   3890  4866 fe040109r1    884 (  0)  0.00 0.11 0.00   47 ( 47)    0 (  0) 
   3974  4939 dg030109r1    733 (  0)  3.39 0.55 0.77   47 ( 60)    5 ( 61) 
   3991  4910 ba110109f1    849 (  0)  0.00 0.11 0.11   27 ( 26)    1 (  1) 
   4021  4954 ch110109f1    841 (  0)  0.77 0.33 0.00   29 ( 29)    0 (  0) 
   4081  5069 fe070109r1    880 (  0)  0.54 0.22 0.00   61 ( 61)    1 ( 15) 
C  4196  5130 ef110109r1    848 (  0)  0.45 0.00 0.11    0 (  0)   49 ( 49) 
   4222  5127 ef120109f1    846 (  0)  0.34 0.00 0.00   33 ( 33)    1 (  1) 
   4231  5174 af010109r1    859 (  0)  0.34 0.00 0.11   54 ( 54)    0 (  0) 
C  4342  5343 cd030109r1    556 (  0)  2.76 0.32 0.00  349 (349)   36 ( 51) 
   4426  5391 ef070109r1    903 (  0)  0.33 0.00 0.00   50 ( 50)    0 (  0) 
   4431  5387 fa080109r1    873 (  0)  0.22 0.45 0.00   57 ( 57)    2 (  0) 
   4483  5451 ed030109r1    909 (  0)  0.22 0.00 0.00   51 ( 51)    0 (  0) 
C  4512  5463 da090109r1    862 (  0)  1.21 0.22 0.00    0 (  8)   46 ( 46) 
   4587  5505 af120109f1    876 (  0)  0.56 0.00 0.00   26 ( 26)    0 (  0) 
C  4644  5621 de070109r1    859 (  0)  1.53 0.33 0.00   15 ( 22)   46 ( 46) 
C  4645  5612 cc040109f1    910 (  0)  0.64 0.21 0.00    0 (  8)   27 ( 27) 
   4704  5659 da070109r1    871 (  0)  0.66 0.22 0.00   50 ( 50)    3 (  3) 
   4768  5732 db090109r1    763 (  0)  1.64 1.29 0.00   46 ( 46)   65 (122) 
C  4888  5856 bd080109r1    888 (  0)  0.44 0.00 0.22    3 (  3)   47 ( 47) 
   4887  5790 be120109f1    810 (  0)  1.49 0.11 0.23   26 ( 49)    4 (  4) 
   4972  5920 fb010109f1    907 (  0)  0.00 0.00 0.00   28 ( 28)    3 (  3) 
C  5008  5958 ed050109f1    902 (  0)  0.33 0.00 0.00    0 (  0)   29 ( 29) 
C  5008  5986 af060109r1    883 (  0)  0.76 0.11 0.11    0 ( 25)   55 ( 55) 
   5048  5966 bg120109r1    808 (  0)  1.04 0.46 0.12   49 ( 49)    2 (  2) 
C  5111  6090 fe040109f1    927 (  0)  0.32 0.00 0.00    0 (  0)   29 (  0) 
C  5150  6094 ef070109f1    806 (  0)  2.85 0.22 0.11    4 ( 36)   29 (  0) 
   5162  6077 be110109f1    873 (  0)  0.00 0.00 0.00   27 ( 26)    0 (  0) 
C  5165  6125 dg030109f1    125 (  0)  34.29 0.32 0.32  194 (422)  140 (161) 
C  5175  6124 ed020109f1    901 (  0)  0.11 0.00 0.00    0 (  0)   30 ( 30) 
C  5284  6262 ec090109r1    880 (  0)  0.44 0.00 0.00    3 (  3)   59 ( 59) 
C  5294  6256 cd020109f1    895 (  0)  0.32 0.00 0.11    0 (  0)   29 ( 29) 
C  5300  6222 ef120109r1    850 (  0)  0.00 0.00 0.00    0 (  0)   50 ( 50) 
C  5387  6360 fe070109f1    903 (  0)  0.21 0.00 0.00    3 (  3)   29 ( 29) 
C  5462  6457 de060109r1    847 (  0)  1.28 0.32 0.00    0 (  0)   59 ( 58) 
   5499  6736 da020109r1    241 (  0)  11.21 1.79 0.22   49 ( 61)  743 (934) 
   5569  6529 fe080109f1    878 (  0)  0.32 0.11 0.00   27 ( 27)    0 (  0) 
   5576  6505 dh110109r1    793 (  0)  1.70 0.11 0.00   47 ( 47)    1 (  1) 
   5651  6618 bf060109r1    867 (  0)  0.22 0.00 0.00   49 ( 49)    0 (  0) 
   5655  6591 ae110109f1    864 (  0)  0.11 0.00 0.00   26 ( 26)    0 (  0) 
C  5685  6640 fa080109f1    850 (  0)  0.65 0.32 0.00    0 (  0)   29 ( 29) 
C  5736  6668 ch110109r1    771 (  0)  2.05 0.11 0.00    1 (  5)   52 ( 52) 
C  5774  6714 bf090109f1    833 (  0)  0.44 0.11 0.00    7 (  0)   28 ( 28) 
   5881  6851 ag070109f1    866 (  0)  0.21 0.11 0.00   36 ( 36)    0 (  0) 
   5887  6873 ad040109r1    853 (  0)  0.54 0.11 0.11   53 ( 57)    0 (  0) 
   5901  6830 ch020109f1    814 (  0)  0.44 0.44 0.00   28 ( 28)    0 (  0) 
   5917  6832 bh020109f1    795 (  0)  0.34 0.00 0.34   28 ( 28)   11 ( 11) 
   5947  6905 aa080109r1    840 (  0)  0.22 0.00 0.00   56 ( 56)    0 (  0) 
   5979  6908 ba020109f1    827 (  0)  0.33 0.11 0.00   30 ( 30)    3 (  3) 
C  6008  6958 ba110109r1    821 (  0)  0.23 0.00 0.11    0 (  0)   63 ( 63) 
   6052  7022 fb040109f1    836 (  0)  1.06 0.32 0.00   29 ( 29)    1 (  1) 
C  6165  7136 ce080109f1    810 (  0)  0.64 1.28 0.00    0 (  5)   33 ( 33) 
C  6264  7208 af010109f1    836 (  0)  0.44 0.00 0.00    6 (  6)   36 ( 36) 
   6271  7217 fc020109r1    819 (  0)  0.11 0.11 0.22   48 ( 62)    0 (  0) 
C  6297  7228 af120109r1    811 (  0)  0.11 0.11 0.11    0 (  0)   58 ( 58) 
   6357  7315 ee090109r1    829 (  0)  0.22 0.11 0.11   50 ( 50)    0 (  0) 
C  6389  7356 fe080109r1    821 (  0)  0.65 0.22 0.11    0 ( 16)   50 ( 50) 
C  6465  7373 bg120109f1    812 (  0)  0.00 0.00 0.00    1 (  1)   30 ( 30) 
C  6500  7415 be120109r1    780 (  0)  0.46 0.12 0.00    0 (  0)   50 ( 50) 
   6522  7448 ed090109f1    793 (  0)  0.11 0.22 0.11   28 ( 28)    0 (  0) 
   6591  7544 fh030109f1    830 (  0)  0.00 0.00 0.11   31 ( 31)    0 (  0) 
   6760  7731 ff050109f1    845 (  0)  0.53 0.11 0.11   28 ( 28)    0 (  0) 
C  6796  7745 bf060109f1    839 (  0)  0.00 0.11 0.00    1 (  1)   29 ( 29) 
C  6795  7740 ba020109r1    797 (  0)  0.34 0.00 0.23    0 (  0)   60 ( 60) 
   6810  7739 bf020109f1    804 (  0)  0.33 0.11 0.11   28 ( 28)    1 (  1) 
C  6812  7761 fb010109r1    820 (  0)  0.22 0.00 0.00    0 (  0)   49 ( 49) 
C  6848  7798 ed030109f1    832 (  0)  0.22 0.00 0.00    0 (  4)   29 ( 29) 
C  6901  7800 be110109r1    614 (  0)  0.89 2.42 0.13   66 (102)   48 ( 48) 
C  7056  7999 ae110109r1    809 (  0)  0.23 0.00 0.00    0 (  0)   59 ( 59) 
C  7095  8060 fb040109r1    807 (  0)  0.33 0.22 0.22    0 (  0)   61 ( 61) 
C  7173  8159 ad040109f1    840 (  0)  0.63 0.00 0.10    0 (  0)   34 ( 34) 
   7182  8130 fc100109f1    837 (  0)  0.00 0.11 0.00   27 ( 27)    0 (  0) 
C  7211  8167 fc020109f1    841 (  0)  0.00 0.11 0.00    2 (  2)   29 ( 29) 
C  7305  8234 ch020109r1    748 (  0)  1.58 0.00 0.34    0 (  0)   44 ( 59) 
C  7465  8412 fh030109r1    831 (  0)  0.44 0.11 0.00    0 (  0)   47 ( 47) 
C  7554  8489 ee090109f1    835 (  0)  0.33 0.00 0.11    0 (  0)   28 ( 28) 
C  7595  8554 dc100109r1    650 (  0)  4.54 1.99 0.22    7 (142)   50 ( 15) 
C  7587  8559 ag070109r1    860 (  0)  0.00 0.00 0.00    2 (  2)   55 ( 20) 
C  7878  8843 aa080109f1    864 (  0)  0.22 0.00 0.00    0 (  0)   37 ( 37) 
   7914  8890 cd080109f1    859 (  0)  0.32 0.21 0.00   32 ( 32)    0 (  0) 
C  8023  9082 cd080109r1    143 (  0)  14.17 1.84 0.79  626 (626)   53 ( 53) 
C  8330  9274 bh020109r1    802 (  0)  0.68 0.00 0.00    0 (  9)   61 ( 61) 
C  8440  9378 db120109r1    812 (  0)  0.34 0.00 0.00    0 (  0)   51 ( 51) 
C  8527  9461 ed090109r1    754 (  0)  1.47 0.23 0.00    0 (  5)   48 ( 48) 
C  8580  9552 ff050109r1    792 (  0)  1.08 0.11 0.32    0 ( 22)   49 ( 49) 
C  8832  9781 fc100109r1    807 (  0)  0.67 0.00 0.00    0 (  0)   50 ( 50) 
C  8911  9829 bf020109r1    820 (  0)  0.87 0.11 0.22    4 ( 18)    0 ( 98) 

Overall discrep rates (%):             1.17 0.20 0.07

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90    6650  67.7    6650  67.7    0.00
 89      13   0.1    6663  67.8    0.00
 88      18   0.2    6681  68.0    0.00
 87      16   0.2    6697  68.1    0.00
 86      25   0.3    6722  68.4    0.00
 85      19   0.2    6741  68.6    0.00
 84      11   0.1    6752  68.7    0.00
 83      17   0.2    6769  68.9    0.00
 82      19   0.2    6788  69.1    0.00
 81      35   0.4    6823  69.4    0.00
 80      11   0.1    6834  69.5    0.00
 79      14   0.1    6848  69.7    0.00
 78      13   0.1    6861  69.8    0.00
 77      23   0.2    6884  70.0    0.00
 76      12   0.1    6896  70.2    0.00
 75      20   0.2    6916  70.4    0.00
 74      11   0.1    6927  70.5    0.00
 73      11   0.1    6938  70.6    0.00
 72       5   0.1    6943  70.6    0.00
 71       3   0.0    6946  70.7    0.00
 70      12   0.1    6958  70.8    0.00
 69      12   0.1    6970  70.9    0.00
 68       7   0.1    6977  71.0    0.00
 67       8   0.1    6985  71.1    0.00
 66    1198  12.2    8183  83.3    0.00
 65      10   0.1    8193  83.4    0.00
 64      10   0.1    8203  83.5    0.00
 63       9   0.1    8212  83.5    0.00
 62       8   0.1    8220  83.6    0.00
 61     639   6.5    8859  90.1    0.00
 60      94   1.0    8953  91.1    0.00
 59       3   0.0    8956  91.1    0.00
 58       5   0.1    8961  91.2    0.00
 57       3   0.0    8964  91.2    0.00
 56      68   0.7    9032  91.9    0.00
 55     138   1.4    9170  93.3    0.00
 54      20   0.2    9190  93.5    0.00
 53     203   2.1    9393  95.6    0.00
 52      78   0.8    9471  96.4    0.00
 51      55   0.6    9526  96.9    0.00
 50      46   0.5    9572  97.4    0.00
 49       7   0.1    9579  97.5    0.00
 48      10   0.1    9589  97.6    0.00
 47      10   0.1    9599  97.7    0.00
 46       1   0.0    9600  97.7    0.00
 45      46   0.5    9646  98.1    0.01
 44       2   0.0    9648  98.2    0.01
 42       2   0.0    9650  98.2    0.01
 41       3   0.0    9653  98.2    0.01
 40      10   0.1    9663  98.3    0.01
 37       5   0.1    9668  98.4    0.01
 35       2   0.0    9670  98.4    0.01
 32       2   0.0    9672  98.4    0.01
 31       2   0.0    9674  98.4    0.01
 -1     155   1.6    9829 100.0  155.01   (quality -1 = terminal quality 0)

Avg. full length: 9829.0, trimmed (qual > -1): 9674.0
Avg. quality: 80.2 per base

Initial, terminal qual 0 segments:  1-75, 9750-9829

Regions of LLR- adjusted quality < 2.0:
1-75, 9750-9829, 

2 regions, avg size 77.5, avg spacing 4914.5

First_start: 76, last_end: 9731

Slack, # used pairs (max_score), unused
 0  1281  (20.4)     1 ( 0.8)     1951
 1   593  (20.2)     0 ( 0.0)      119
 2   108  (19.8)     0 ( 0.0)        1
 3    47  (15.8)     0 ( 0.0)        0
 4    25  (15.1)     0 ( 0.0)        0
 5     7  (10.1)     0 ( 0.0)        0
 6     3  ( 6.6)     0 ( 0.0)        0
 7     2  (13.8)     0 ( 0.0)        0
 8     3  ( 5.4)     0 ( 0.0)        0
11     1  ( 2.7)     0 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 8891 - right      939+      cd080109f1   (7914)    No           1915+

Bottom strand: 
 left -  1769     1769+      fe010109r1   (2707)    No           2707+
 9830 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  19289  19289 128514 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1845 (1.44)
51  12100  31389 109225 ( 84.99)     0  0    0   0   0   0     0 (0.00)    0  1845 (1.69)
50   3677  35066  97125 ( 75.58)     0  0    0   0   0   0     0 (0.00)    0  1845 (1.90)
48    583  35649  93448 ( 72.71)     0  0    0   0   0   0     0 (0.00)    0  1845 (1.97)
47    475  36124  92865 ( 72.26)     0  0    0   0   0   0     0 (0.00)    0  1845 (1.99)
46   2591  38715  92390 ( 71.89)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.00)
45   4179  42894  89799 ( 69.87)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.05)
44   2876  45770  85620 ( 66.62)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.15)
43   7273  53043  82744 ( 64.39)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.23)
42   9663  62706  75471 ( 58.73)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.44)
41   2535  65241  65808 ( 51.21)     0  0    0   0   0   0     0 (0.00)    0  1845 (2.80)
40   8547  73788  63273 ( 49.23)    10  0    0   0   0   0     0 (0.00)    0  1845 (2.92)
39    745  74533  54726 ( 42.58)     1  0    0   0   0   0     0 (0.00)    0  1845 (3.37)
38   1154  75687  53981 ( 42.00)     0  0    0   0   0   0     0 (0.00)    0  1845 (3.42)
37   3496  79183  52827 ( 41.11)     6  0    0   0   0   0     0 (0.00)    0  1845 (3.49)
36    417  79600  49331 ( 38.39)     1  0    0   0   0   0     0 (0.00)    0  1845 (3.74)
35   4366  83966  48914 ( 38.06)    16  0    0   0   0   0     0 (0.00)    0  1845 (3.77)
34   1128  85094  44548 ( 34.66)    17  0    0   0   0   0     0 (0.00)    0  1845 (4.14)
33   1457  86551  43420 ( 33.79)    12  0    0   0   0   0     0 (0.00)    0  1845 (4.25)
32   1712  88263  41963 ( 32.65)    13  0    0   0   1   0     1 (0.06)    1  1845 (4.40)
31    647  88910  40251 ( 31.32)    10  0    0   1   0   0     1 (0.15)    2  1844 (4.58)
30    725  89635  39604 ( 30.82)     7  0    0   0   0   0     0 (0.00)    2  1843 (4.65)
29   2852  92487  38879 ( 30.25)    64  0    0   0   0   0     0 (0.00)    2  1843 (4.74)
28    810  93297  36027 ( 28.03)    10  0    0   0   0   0     0 (0.00)    2  1843 (5.12)
27   1280  94577  35217 ( 27.40)    49  0    0   2   0   0     2 (0.16)    4  1843 (5.23)
26    649  95226  33937 ( 26.41)    15  0    0   0   0   0     0 (0.00)    4  1841 (5.42)
25   1676  96902  33288 ( 25.90)    55  0    0   0   0   0     0 (0.00)    4  1841 (5.53)
24   1424  98326  31612 ( 24.60)    39  0    0   1   1   0     2 (0.14)    6  1841 (5.82)
23   1047  99373  30188 ( 23.49)    30  0    0   1   0   0     1 (0.10)    7  1839 (6.09)
22    997 100370  29141 ( 22.68)    57  0    0   2   0   1     3 (0.30)   10  1838 (6.31)
21   1252 101622  28144 ( 21.90)    18  0    0   0   2   1     3 (0.24)   13  1835 (6.52)
20   1118 102740  26892 ( 20.93)    40  0    0   1   1   0     2 (0.18)   15  1832 (6.81)
19   1756 104496  25774 ( 20.06)    94  0    0   9   1   1    11 (0.63)   26  1830 (7.10)
18   1204 105700  24018 ( 18.69)    25  0    0   3   4   0     7 (0.58)   33  1819 (7.57)
17   1088 106788  22814 ( 17.75)    48  0    0   5   2   0     7 (0.64)   40  1812 (7.94)
16   1151 107939  21726 ( 16.91)    72  0    0  13   3   1    17 (1.48)   57  1805 (8.31)
15   1665 109604  20575 ( 16.01)    41  0    0  11   4   1    16 (0.96)   73  1788 (8.69)
14   1189 110793  18910 ( 14.71)    31  0    0  13   7   1    21 (1.77)   94  1772 (9.37)
13   1580 112373  17721 ( 13.79)    61  0    0  29   7   5    41 (2.59)  135  1751 (9.88)
12   1574 113947  16141 ( 12.56)    11  0    0  27  11   4    42 (2.67)  177  1710 (10.59)
11   1970 115917  14567 ( 11.33)    26  0    0  63  14   9    86 (4.37)  263  1668 (11.45)
10   2704 118621  12597 (  9.80)    52  0    0 104  29  11   144 (5.33)  407  1582 (12.56)
 9   3862 122483   9893 (  7.70)    80  0    0 291  45  32   368 (9.53)  775  1438 (14.54)
 8   2458 124941   6031 (  4.69)    68  0    0 214  41  15   270 (10.98)  1045  1070 (17.74)
 7   2075 127016   3573 (  2.78)    57  0    0 227  47   7   281 (13.54)  1326  800 (22.39)
 6    751 127767   1498 (  1.17)    30  0    0 117  21   4   142 (18.91)  1468  519 (34.65)
 4    456 128223    747 (  0.58)     9  0    0  81   2   1    84 (18.42)  1552  377 (50.47)
 0    291 128514    291 (  0.23)     1  0   287   0   4   2   293 (100.69)  1845  293 (100.69)
-1     84 128598      0 (  0.00)  9016  0    0   1   2   0     3 (3.57)  1848    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90  98971  98971 125819 (100.00)     0  0    0   0   0   0     0 (0.00)    0  1186 (0.94)
89     76  99047  26848 ( 21.34)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.42)
88    160  99207  26772 ( 21.28)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.43)
87    103  99310  26612 ( 21.15)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.46)
86    183  99493  26509 ( 21.07)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.47)
85    129  99622  26326 ( 20.92)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.51)
84     54  99676  26197 ( 20.82)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.53)
83    117  99793  26143 ( 20.78)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.54)
82    109  99902  26026 ( 20.69)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.56)
81    271 100173  25917 ( 20.60)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.58)
80     91 100264  25646 ( 20.38)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.62)
79     69 100333  25555 ( 20.31)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.64)
78     37 100370  25486 ( 20.26)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.65)
77    104 100474  25449 ( 20.23)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.66)
76     62 100536  25345 ( 20.14)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.68)
75     67 100603  25283 ( 20.09)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.69)
74     30 100633  25216 ( 20.04)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.70)
73     63 100696  25186 ( 20.02)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.71)
72     13 100709  25123 ( 19.97)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.72)
71     27 100736  25110 ( 19.96)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.72)
70     40 100776  25083 ( 19.94)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.73)
69     41 100817  25043 ( 19.90)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.74)
68     19 100836  25002 ( 19.87)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.74)
67     27 100863  24983 ( 19.86)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.75)
66   6415 107278  24956 ( 19.83)     0  0    0   0   0   0     0 (0.00)    0  1186 (4.75)
65    130 107408  18541 ( 14.74)     0  0    0   0   0   0     0 (0.00)    0  1186 (6.40)
64     44 107452  18411 ( 14.63)     0  0    0   0   0   0     0 (0.00)    0  1186 (6.44)
63     12 107464  18367 ( 14.60)     0  0    0   0   0   0     0 (0.00)    0  1186 (6.46)
62     40 107504  18355 ( 14.59)     0  0    0   0   0   0     0 (0.00)    0  1186 (6.46)
61   3095 110599  18315 ( 14.56)     0  0    0   0   0   0     0 (0.00)    0  1186 (6.48)
60    569 111168  15220 ( 12.10)     0  0    0   0   0   0     0 (0.00)    0  1186 (7.79)
59    120 111288  14651 ( 11.64)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.10)
58     77 111365  14531 ( 11.55)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.16)
57     97 111462  14454 ( 11.49)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.21)
56    434 111896  14357 ( 11.41)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.26)
55    698 112594  13923 ( 11.07)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.52)
54    368 112962  13225 ( 10.51)     0  0    0   0   0   0     0 (0.00)    0  1186 (8.97)
53   1052 114014  12857 ( 10.22)     0  0    0   0   0   0     0 (0.00)    0  1186 (9.22)
52    556 114570  11805 (  9.38)     0  0    0   0   0   0     0 (0.00)    0  1186 (10.05)
51    294 114864  11249 (  8.94)     0  0    0   0   0   0     0 (0.00)    0  1186 (10.54)
50    246 115110  10955 (  8.71)     0  0    0   0   0   0     0 (0.00)    0  1186 (10.83)
49    116 115226  10709 (  8.51)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.07)
48    125 115351  10593 (  8.42)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.20)
47    103 115454  10468 (  8.32)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.33)
46    100 115554  10365 (  8.24)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.44)
45    243 115797  10265 (  8.16)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.55)
44    155 115952  10022 (  7.97)     0  0    0   0   0   0     0 (0.00)    0  1186 (11.83)
43    102 116054   9867 (  7.84)     0  0    0   0   0   0     0 (0.00)    0  1186 (12.02)
42    149 116203   9765 (  7.76)     0  0    0   0   0   0     0 (0.00)    0  1186 (12.15)
41    145 116348   9616 (  7.64)     0  0    0   0   0   0     0 (0.00)    0  1186 (12.33)
40   2471 118819   9471 (  7.53)     0  0    0   0   0   0     0 (0.00)    0  1186 (12.52)
39     50 118869   7000 (  5.56)     0  0    0   0   0   0     0 (0.00)    0  1186 (16.94)
38     17 118886   6950 (  5.52)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.06)
37     38 118924   6933 (  5.51)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.11)
36     24 118948   6895 (  5.48)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.20)
35     38 118986   6871 (  5.46)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.26)
34     63 119049   6833 (  5.43)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.36)
33     52 119101   6770 (  5.38)     0  0    0   0   0   0     0 (0.00)    0  1186 (17.52)
32     52 119153   6718 (  5.34)     0  0    0   0   1   0     1 (1.92)    1  1186 (17.65)
31     33 119186   6666 (  5.30)     0  0    0   1   0   0     1 (3.03)    2  1185 (17.78)
30     27 119213   6633 (  5.27)     0  0    0   1   0   0     1 (3.70)    3  1184 (17.85)
29     89 119302   6606 (  5.25)     0  0    0   0   0   0     0 (0.00)    3  1183 (17.91)
28     24 119326   6517 (  5.18)     0  0    0   0   0   0     0 (0.00)    3  1183 (18.15)
27     93 119419   6493 (  5.16)     0  0    0   3   0   0     3 (3.23)    6  1183 (18.22)
26     53 119472   6400 (  5.09)     0  0    0   1   0   0     1 (1.89)    7  1180 (18.44)
25    289 119761   6347 (  5.04)     0  0    0   1   0   1     2 (0.69)    9  1179 (18.58)
24    106 119867   6058 (  4.81)     0  0    0   0   1   0     1 (0.94)   10  1177 (19.43)
23     66 119933   5952 (  4.73)     0  0    0   2   0   0     2 (3.03)   12  1176 (19.76)
22     45 119978   5886 (  4.68)     1  0    0   3   0   0     3 (6.67)   15  1174 (19.95)
21     83 120061   5841 (  4.64)     0  0    0   0   1   1     2 (2.41)   17  1171 (20.05)
20    102 120163   5758 (  4.58)     0  0    0   1   1   0     2 (1.96)   19  1169 (20.30)
19    218 120381   5656 (  4.50)     0  0    0   5   1   1     7 (3.21)   26  1167 (20.63)
18     53 120434   5438 (  4.32)     1  0    0   1   3   0     4 (7.55)   30  1160 (21.33)
17    106 120540   5385 (  4.28)     0  0    0   5   2   0     7 (6.60)   37  1156 (21.47)
16    157 120697   5279 (  4.20)     0  0    0   8   1   1    10 (6.37)   47  1149 (21.77)
15    174 120871   5122 (  4.07)     0  0    0  15   4   0    19 (10.92)   66  1139 (22.24)
14    167 121038   4948 (  3.93)     0  0    0  11   5   1    17 (10.18)   83  1120 (22.64)
13    282 121320   4781 (  3.80)     2  0    0  21   7   4    32 (11.35)  115  1103 (23.07)
12    259 121579   4499 (  3.58)     0  0    0  16   8   4    28 (10.81)  143  1071 (23.81)
11    416 121995   4240 (  3.37)     0  0    0  49  14   9    72 (17.31)  215  1043 (24.60)
10    562 122557   3824 (  3.04)     0  0    0  73  21   7   101 (17.97)  316  971 (25.39)
 9   1100 123657   3262 (  2.59)     2  0    0 155  26  21   202 (18.36)  518  870 (26.67)
 8    692 124349   2162 (  1.72)     3  0    0 133  32  11   176 (25.43)  694  668 (30.90)
 7    800 125149   1470 (  1.17)     5  0    0 179  41   7   227 (28.38)  921  492 (33.47)
 6    312 125461    670 (  0.53)     0  0    0  79  16   3    98 (31.41)  1019  265 (39.55)
 4    231 125692    358 (  0.28)     0  0    0  37   1   0    38 (16.45)  1057  167 (46.65)
 0    127 125819    127 (  0.10)     0  0   123   0   4   2   129 (101.57)  1186  129 (101.57)
-1   2779 128598      0 (  0.00)  10178  0   164 416  59  23   662 (23.82)  1848    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     155      155        2
 31       2      157        2
 32       2      159        2
 35       2      161        2
 37       5      166        4
 40      10      176        6
 41       3      179        7
 42       2      181        7
 44       2      183        7
 45      46      229       16
 46       1      230       16
 47      10      240       16
 48      10      250       20
 49       7      257       21
 50      46      303       34
 51      55      358       42
 52      78      436       67
 53     203      639      108
 54      20      659      116
 55     138      797      128
 56      68      865      128
 57       3      868      127
 58       5      873      126
 59       3      876      127
 60      94      970      142
 61     639     1609      183
 62       8     1617      184
 63       9     1626      189
 64      10     1636      187
 65      10     1646      189
 66    1198     2844       19
 67       8     2852       17
 68       7     2859       18
 69      12     2871       18
 70      12     2883       21
 71       3     2886       22
 72       5     2891       23
 73      11     2902       22
 74      11     2913       25
 75      20     2933       28
 76      12     2945       34
 77      23     2968       35
 78      13     2981       35
 79      14     2995       36
 80      11     3006       35
 81      35     3041       40
 82      19     3060       40
 83      17     3077       40
 84      11     3088       41
 85      19     3107       38
 86      25     3132       41
 87      16     3148       42
 88      18     3166       41
 89      13     3179       40
 90    6650     9829        1

SS region: 2708 (27.55%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 4249     -3.0  [-3.0,  0.0]  (0, 1)
 4284     -3.1  [-3.1,  0.0]  (0, 1)
 4420     -3.1  [-3.1,  0.0]  (0, 1)
 4767     -3.2  [-3.2,  0.0]  (0, 1)
 7344     -3.4  [-3.4,  0.0]  (0, 1)
 7717     -3.4  [-3.4,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  8649- 9029 [-2.1] (0,0)   C cd080109r1         438-54 || local(+/-) (6.8,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -9.4 (<20 part: -9.4 (#=64), >20:0.0 (#=0); in HQ: -2.1, out HQ -7.3), match: 7.2  trail: 0.0  lead: 0.0  total: -2.2 

Gaps in unique-read coverage:  None.

Contig 13.  192 reads; 14159 bp (untrimmed), 14130 (trimmed).
    -55   974 ce090109r1    358 (  0)  4.93 3.40 0.17   58 ( 58)  384 (548) 
    -38   927 af100109f1    832 (  0)  0.22 0.32 0.00   39 ( 41)    3 (  3) 
     83  1035 eg100109r1    826 (  0)  0.44 0.00 0.00   51 ( 51)    0 (  0) 
     90  1011 fe110109r1    787 (  0)  0.35 0.12 0.12   50 ( 50)    5 (  4) 
    199  1148 ca030109r1    660 (  0)  3.94 1.24 0.11   62 ( 62)    0 (  0) 
    243  1148 fh120109r1    770 (  0)  0.35 0.23 0.00   51 ( 51)    0 (  0) 
    470  1408 da110109r1    749 (  0)  1.24 0.34 0.22   49 ( 49)    1 ( 35) 
    813  1753 eg080109f1    785 (  0)  0.88 0.22 0.00   29 ( 29)    0 ( 14) 
    834  1818 ed040109r1    827 (  0)  0.32 0.00 0.00   49 ( 49)    0 (  0) 
    849  1813 ad110109f1    805 (  0)  0.11 0.11 0.00   55 ( 55)    1 (  1) 
    881  1839 cc020109r1    760 (  0)  0.78 0.11 0.22   62 ( 62)    0 ( 15) 
   1019  1977 cf090109f1    764 (  0)  1.63 0.22 0.22   34 ( 61)    4 ( 22) 
   1070  1987 ff120109f1    797 (  0)  0.11 0.00 0.00   30 ( 30)    0 (  0) 
   1193  2156 aa050109f1    833 (  0)  0.32 0.00 0.00   36 ( 36)    2 (  0) 
   1218  2180 dh080109f1    658 (  0)  4.33 0.23 0.47  100 (133)    9 ( 17) 
   1230  2192 fc070109f1    714 (  0)  4.82 0.11 0.00   30 ( 30)    0 (  5) 
   1454  2414 db070109r1    823 (  0)  0.66 0.22 0.00   47 ( 47)    8 (  8) 
   1455  2342 bf110109r1    746 (  0)  0.73 0.00 0.12   49 ( 49)   14 (  8) 
   1499  2456 ac010109f1    464 (  0)  13.58 1.31 0.11   41 ( 41)    4 ( 15) 
   1504  2437 bc010109f1    835 (  0)  0.11 0.11 0.11   31 ( 31)    0 (  0) 
C  1696  2659 af100109r1    885 (  0)  0.00 0.00 0.00    0 (  0)   54 ( 54) 
C  1727  2688 ce090109f1    888 (  0)  0.22 0.11 0.11    4 (  4)   29 ( 29) 
   1789  2737 fd100109r1    857 (  0)  0.78 0.00 0.00   51 ( 62)    0 (  9) 
   2034  3004 cb040109r1    811 (  0)  1.91 0.34 0.11   49 ( 49)   30 ( 86) 
C  2074  2999 eg100109f1    731 (  0)  2.78 1.16 0.12   30 ( 99)   32 ( 32) 
   2072  3019 fb100109r1    767 (  0)  3.57 0.45 0.00   51 ( 51)    0 (  0) 
C  2100  3034 fe110109f1    892 (  0)  0.11 0.00 0.00    1 (  1)   26 ( 26) 
C  2104  3076 dg050109r1    882 (  0)  0.65 0.22 0.11    0 (  0)   46 ( 46) 
C  2143  3054 fh120109f1    840 (  0)  0.80 0.00 0.11    5 (  5)   27 ( 27) 
C  2171  3131 ed040109f1    904 (  0)  0.32 0.11 0.00    0 (  0)   27 ( 27) 
C  2178  3145 dh080109r1    820 (  0)  2.30 0.22 0.11    4 ( 23)   51 ( 62) 
   2224  3129 ee120109f1    862 (  0)  0.11 0.00 0.00   24 ( 28)    2 (  2) 
C  2236  3179 cc020109f1    895 (  0)  0.33 0.00 0.00    0 (  0)   24 ( 24) 
C  2259  3238 cf090109r1    529 (  0)  5.99 1.77 0.14  197 (300)   49 ( 81) 
C  2305  3255 ca030109f1    869 (  0)  1.09 0.11 0.00    0 (  0)   31 ( 66) 
   2343  3328 fd040109r1    887 (  0)  0.32 0.22 0.00   52 ( 52)    9 (  9) 
C  2387  3342 fc070109r1    663 (  0)  6.93 0.44 0.33    1 ( 74)   46 ( 46) 
C  2450  3364 ff120109r1    807 (  0)  1.04 0.35 0.00    1 ( 11)   47 ( 51) 
   2564  3511 dh100109r1    829 (  0)  0.67 0.22 0.11   52 ( 52)    1 (  1) 
C  2579  3539 eg080109r1    848 (  0)  0.55 0.11 0.11    4 ( 22)   49 ( 49) 
   2604  3556 bb090109r1    871 (  0)  0.00 0.00 0.00   50 ( 50)    0 (  0) 
   2643  3586 bb030109f1    847 (  0)  0.66 0.22 0.11   27 ( 27)    6 (  0) 
   2718  3646 eh110109r1    840 (  0)  0.23 0.11 0.00   51 ( 51)    0 (  0) 
C  2728  3671 ad110109r1    857 (  0)  0.11 0.00 0.00    0 (  0)   54 ( 54) 
   2827  3791 eg040109r1    859 (  0)  0.22 0.00 0.11   52 ( 56)    0 (  0) 
C  2829  3791 aa050109r1    859 (  0)  0.11 0.11 0.11    0 (  0)   54 ( 54) 
C  2858  3803 fd100109f1    868 (  0)  0.11 0.00 0.11    0 (  0)   26 ( 22) 
   2947  3923 ef050109r1    853 (  0)  0.43 0.32 0.00   51 ( 51)    0 (  0) 
   2982  3969 ad060109f1    880 (  0)  0.63 0.00 0.10   34 ( 34)    0 (  0) 
C  3081  3998 bf110109f1    833 (  0)  0.11 0.11 0.00    0 (  0)   30 ( 30) 
   3129  4103 ae080109r1    846 (  0)  0.98 0.00 0.00   58 ( 58)    0 ( 26) 
   3155  4118 fg050109r1    840 (  0)  0.99 0.00 0.00   47 ( 47)    7 (  7) 
   3222  4166 eg110109r1    840 (  0)  0.11 0.00 0.00   63 ( 63)    0 (  0) 
C  3247  4209 ac010109r1    464 (  0)  11.30 1.69 0.34    1 ( 35)   77 (114) 
C  3249  4201 bc010109r1    847 (  0)  0.33 0.11 0.11    0 (  0)   50 ( 50) 
C  3366  4247 ee120109r1    667 (  0)  1.07 0.67 0.13   86 ( 99)   49 ( 49) 
   3398  4429 db020109r1    463 (  0)  4.49 0.67 0.33   31 ( 51)  400 (400) 
   3421  4355 ba030109f1    863 (  0)  0.44 0.00 0.00   33 ( 33)    1 (  1) 
C  3439  4388 fb100109f1    805 (  0)  2.93 0.11 0.00    0 (  0)   29 ( 29) 
C  3455  4423 cb040109f1    906 (  0)  0.32 0.00 0.00    0 (  0)   28 ( 28) 
   3510  4467 fh080109f1    883 (  0)  0.64 0.21 0.00   26 ( 26)    0 ( 26) 
   3512  4480 dh030109r1    871 (  0)  0.33 0.11 0.11   59 ( 59)    1 (  1) 
   3553  4472 ea100109f1    858 (  0)  0.00 0.22 0.11   29 ( 27)    0 (  0) 
C  3586  4520 eg110109f1    626 (  0)  3.46 0.80 0.27  153 (229)   31 ( 50) 
   3648  4628 af050109f1    889 (  0)  0.43 0.53 0.00   35 ( 35)    5 (  1) 
   3660  4624 fd030109f1    897 (  0)  0.11 0.43 0.00   29 ( 29)    0 (  0) 
   3862  4812 bc100109r1    872 (  0)  0.22 0.11 0.11   50 ( 50)    0 (  0) 
C  3869  4851 fd040109f1    926 (  0)  0.42 0.00 0.00    0 (  0)   29 ( 29) 
C  3907  4913 ad060109r1    893 (  0)  0.75 0.11 0.00    1 (  1)   72 ( 72) 
C  3954  4937 ae080109f1    907 (  0)  0.11 0.11 0.21    0 (  0)   42 ( 42) 
   3967  4910 ah020109r1    861 (  0)  0.11 0.00 0.11   57 ( 16)    2 (  2) 
   3971  4905 df010109r1    745 (  0)  2.87 0.69 0.23   58 (  8)    5 ( 44) 
C  3983  4923 dh100109f1    724 (  0)  3.03 0.12 0.24    9 ( 30)  108 (152) 
   4016  4981 bf080109r1    893 (  0)  0.11 0.00 0.00   50 ( 50)    0 (  0) 
   4044  5003 cf070109f1    857 (  0)  1.70 0.00 0.21   21 ( 21)    0 (  6) 
   4085  5028 bg020109r1    791 (  0)  2.12 0.67 0.00   48 ( 59)    0 (  0) 
   4124  5084 cg090109r1    727 (  0)  3.17 1.02 0.34   48 ( 61)   30 (143) 
   4176  5154 dd080109r1    885 (  0)  0.54 0.11 0.11   47 ( 47)    0 (  4) 
C  4185  5123 eg040109f1    777 (  0)  2.52 0.99 0.11    0 ( 87)   26 ( 26) 
C  4216  5189 dg060109r1    839 (  0)  1.63 0.54 0.00    4 ( 42)   47 ( 47) 
C  4303  5210 eh110109f1    838 (  0)  0.34 0.11 0.00    0 (  0)   28 ( 28) 
C  4390  5321 bb090109f1    840 (  0)  0.22 0.44 0.11    1 (  1)   28 ( 28) 
C  4398  5350 ef050109f1    848 (  0)  1.19 0.00 0.11    0 (  0)   28 ( 28) 
C  4457  5412 bb030109r1    832 (  0)  0.66 0.44 0.00    0 (  0)   50 ( 50) 
C  4557  5488 bc100109f1    856 (  0)  0.22 0.00 0.00    0 (  0)   32 ( 29) 
C  4573  5509 ah020109f1    857 (  0)  0.11 0.00 0.11    0 (  0)   33 ( 33) 
C  4765  5725 fh080109r1    843 (  0)  0.66 0.00 0.00    3 (  3)   50 ( 50) 
C  5278  6249 fg050109f1    881 (  0)  0.32 0.11 0.00    0 (  0)   30 ( 30) 
C  5306  6289 af050109r1    871 (  0)  0.32 0.11 0.00    0 (  0)   54 ( 54) 
C  5321  6588 cf070109r1     83 (  0)  11.63 8.14 0.00  948 (1121)   62 (118) 
C  5330  6302 dd080109f1    375 (  0)  15.80 0.26 0.13   69 (128)  132 (415) 
   5349  6281 fh100109r1    809 (  0)  0.91 0.11 0.00   50 ( 59)    0 (  0) 
C  5361  6297 bf080109f1    858 (  0)  0.33 0.00 0.00    2 (  2)   23 ( 23) 
C  5415  6375 cg090109f1    845 (  0)  1.18 0.00 0.00    0 (  0)   28 ( 28) 
C  5543  6507 fd030109r1    865 (  0)  0.22 0.00 0.11    0 (  0)   49 ( 49) 
   5598  6615 cd090109r1    272 (  0)  7.04 1.64 0.23   55 ( 55)  537 (547) 
C  5659  6585 bg020109f1    849 (  0)  0.67 0.00 0.00    0 (  0)   25 ( 25) 
   5731  6641 bd120109f1    845 (  0)  0.11 0.11 0.00   29 ( 29)    0 (  0) 
   5950  6925 bf050109r1    857 (  0)  0.65 0.11 0.32   50 ( 50)    0 (  0) 
   5970  6944 ef080109r1    766 (  0)  1.98 1.54 0.11   53 ( 53)   12 ( 78) 
   5981  6962 dc090109r1    712 (  0)  4.10 0.68 0.23   43 (  8)   62 (166) 
   5982  6967 bd060109r1    883 (  0)  0.53 0.11 0.00   50 (  7)    0 (  0) 
C  6081  7001 ea100109r1    808 (  0)  0.69 0.23 0.12    5 (  5)   47 ( 47) 
   6295  7253 fh060109f1    880 (  0)  0.00 0.00 0.00   29 ( 29)    6 (  6) 
C  6403  7337 df010109f1    271 (  0)  34.05 0.00 0.00   13 (383)   85 (209) 
   6440  7403 fg070109r1    828 (  0)  0.66 0.33 0.00   50 ( 50)    5 (  5) 
   6685  7631 bd100109r1    853 (  0)  0.22 0.00 0.00   49 ( 49)    0 (  0) 
C  6788  7730 fh100109f1    870 (  0)  0.22 0.00 0.00    0 (  0)   30 ( 30) 
   6789  7773 de050109f1    833 (  0)  1.68 0.42 0.31   30 ( 30)    1 ( 10) 
   6818  7776 ah030109r1    861 (  0)  0.11 0.00 0.00   56 ( 56)    0 (  0) 
   6928  7902 bc060109r1    832 (  0)  0.65 0.65 0.11   51 ( 51)    4 (  4) 
   6939  7903 bg060109r1    842 (  0)  0.87 0.33 0.00   47 ( 46)    0 ( 26) 
   6956  7892 ea050109f1    824 (  0)  1.10 0.22 0.11   30 ( 29)    0 (  3) 
C  7097  8016 cg120109r1     98 (  0)  18.16 2.88 0.00  499 (645)   74 ( 74) 
   7215  8162 eb080109r1    670 (  0)  1.85 0.53 0.00   50 ( 50)  142 (169) 
   7302  8201 fe120109f1    828 (  0)  0.34 0.00 0.11   22 ( 22)    0 (  0) 
   7310  8258 eg050109f1    682 (  0)  5.18 1.21 0.11   28 ( 66)   14 (142) 
C  7312  8265 bd060109f1    868 (  0)  0.32 0.11 0.22    0 (  4)   26 ( 26) 
C  7317  8256 bf050109f1    867 (  0)  0.33 0.00 0.11    0 (  0)   25 ( 25) 
   7359  8273 ca120109f1    814 (  0)  1.13 0.00 0.00   28 ( 32)    2 (  2) 
C  7426  8348 bd120109r1    811 (  0)  0.57 0.23 0.11    5 ( 27)   43 ( 43) 
C  7601  8543 ef080109f1    815 (  0)  1.20 0.44 0.11    0 (  8)   27 ( 27) 
C  7617  8570 cd090109f1    852 (  0)  0.32 0.22 0.11    0 (  0)   28 ( 28) 
C  7635  8604 fh060109r1    842 (  0)  0.33 0.00 0.11    0 (  0)   64 ( 64) 
   7812  8774 cb030109r1    810 (  0)  1.97 0.11 0.00   47 ( 51)    0 ( 34) 
   7881  8833 aa020109r1    852 (  0)  0.33 0.00 0.00   53 ( 56)    0 (  0) 
   7907  8859 ea060109f1    505 (  0)  5.60 1.96 0.00   31 ( 31)  208 (396) 
C  8015  8977 ah030109f1    885 (  0)  0.22 0.00 0.00    0 (  0)   34 ( 34) 
   8089  9064 ab060109r1    874 (  0)  0.43 0.00 0.11   55 ( 55)    0 (  0) 
   8115  9070 fe100109f1    866 (  0)  0.65 0.22 0.11   26 ( 26)    0 (  8) 
   8136  9124 bg110109r1    473 (  0)  1.82 2.64 0.33   50 ( 50)  333 (403) 
C  8203  9170 fg070109f1    888 (  0)  0.43 0.00 0.00    0 (  0)   30 ( 30) 
   8526  9453 bg100109f1    748 (  0)  2.45 0.67 0.22   31 ( 58)    0 ( 78) 
C  8575  9478 fe120109r1    802 (  0)  0.23 0.00 0.12    0 (  0)   50 ( 50) 
C  8577  9546 eg050109r1    863 (  0)  0.11 0.22 0.00    0 (  0)   50 ( 50) 
   8700  9651 fh040109r1    830 (  0)  0.22 0.00 0.00   61 ( 61)    0 (  0) 
C  8715  9630 ca120109r1    713 (  0)  1.95 1.03 0.34    0 (  0)   45 ( 59) 
C  8725  9654 bd100109f1    831 (  0)  0.33 0.11 0.00    0 (  0)   28 ( 28) 
C  8736  9700 ea050109r1    837 (  0)  0.33 0.00 0.00    1 (  1)   60 ( 60) 
C  8792  9781 de050109r1    721 (  0)  3.31 1.28 0.21    4 (107)   49 ( 49) 
C  8902  9845 bg060109f1    853 (  0)  0.11 0.00 0.00    0 (  0)   23 ( 23) 
   9012  9973 ah060109f1    835 (  0)  0.11 0.43 0.11   34 ( 44)    7 (  7) 
   9070 10019 fa050109r1    837 ( 31)  0.22 0.00 0.00   50 ( 50)    0 (  0) 
   9122 10053 bd110109r1    828 ( 31)  0.11 0.00 0.00   53 ( 55)    0 (  0) 
   9165 10093 cf010109f1    824 ( 31)  0.89 0.00 0.00   29 ( 50)    0 (  0) 
C  9237 10199 ea060109r1    829 ( 31)  0.99 0.22 0.00    0 (  0)   50 ( 50) 
   9369 10338 cf050109f1    835 ( 31)  0.96 0.96 0.11   27 ( 27)    9 ( 50) 
C  9408 10365 fe100109r1    851 ( 31)  0.55 0.33 0.11    0 (  0)   48 ( 48) 
   9440 10381 eg070109f1    830 ( 31)  1.21 0.55 0.00   28 ( 28)    5 (  5) 
   9449 10390 ch060109r1    535 (  0)  6.00 0.70 0.00   42 ( 64)  183 (307) 
   9467 10425 cc030109r1    840 ( 31)  0.77 0.33 0.22   49 ( 49)    3 ( 30) 
C  9608 10559 eb080109f1    885 ( 48)  0.33 0.22 0.00    0 (  0)   29 ( 29) 
C  9641 10605 cb030109f1    893 ( 31)  0.53 0.11 0.21    0 (  0)   26 ( 26) 
   9680 10653 fd050109f1    926 ( 31)  0.21 0.11 0.00   28 ( 28)    0 (  0) 
C  9714 10669 bc060109f1    824 ( 70)  2.16 0.97 0.00    0 ( 89)   29 ( 29) 
C  9728 10684 aa020109f1    913 ( 31)  0.00 0.00 0.00    0 (  0)   36 ( 36) 
C  9796 10778 bg100109r1    514 (  0)  6.62 1.89 0.27  182 (285)   61 ( 61) 
C  9792 10786 ab060109f1    918 ( 31)  0.53 0.11 0.00    0 (  0)   50 ( 50) 
  10009 10969 bg040109r1    887 (  0)  0.22 0.00 0.22   49 ( 49)    0 (  0) 
C 10257 11189 cf010109r1    805 ( 92)  1.27 0.58 0.00   15 ( 34)   50 ( 50) 
  10329 11293 bd020109r1    875 (  0)  0.66 0.11 0.00   50 ( 50)   10 ( 17) 
C 10431 11334 bg110109f1    868 (144)  0.00 0.00 0.00    0 (  0)   28 ( 28) 
C 10544 11506 ah060109r1    898 (  0)  0.11 0.00 0.00    0 (  0)   54 ( 54) 
  10566 11541 ac040109r1    865 (210)  1.41 0.00 0.22   53 ( 53)    0 ( 36) 
  10703 11673 dd100109r1    657 (152)  3.01 0.27 0.00   50 ( 50)  189 (189) 
C 10808 11762 fh040109f1    910 (224)  0.22 0.00 0.00    0 (  0)   29 ( 29) 
C 10858 11832 fd050109r1    911 (224)  0.11 0.00 0.00    1 (  1)   50 ( 50) 
C 10879 11826 fa050109f1    893 (215)  0.65 0.00 0.00    4 ( 12)   22 ( 22) 
C 10967 11924 ch060109f1    896 ( 59)  0.64 0.00 0.11    0 (  0)   27 ( 27) 
C 10987 11914 ag120109f1    558 ( 41)  0.00 0.00 0.00  326 (326)   35 ( 19) 
C 10990 11905 bd110109f1    873 ( 45)  0.11 0.00 0.00    0 (  0)   30 ( 30) 
C 11047 12013 cc030109f1    912 (  0)  0.53 0.00 0.00    0 (  0)   29 ( 33) 
C 11134 12074 bg040109f1    898 (  0)  0.00 0.00 0.00    0 (  0)   29 ( 29) 
  11258 12184 ag120109r1    558 ( 41)  0.00 0.00 0.00   55 ( 55)  305 (289) 
C 11335 12279 bd020109f1    889 (  0)  0.33 0.11 0.00    0 (  0)   29 ( 29) 
C 11347 12314 eg070109r1    885 (  0)  0.65 0.00 0.00    1 (  1)   50 ( 52) 
  11669 12684 cd060109r1    333 (  0)  11.93 1.19 0.34   51 ( 99)  378 (503) 
  11822 12987 df030109r1    336 (  0)  5.37 0.00 0.00   86 ( 86)  670 (670) 
C 12018 12971 dd100109f1    885 (  0)  0.76 0.11 0.00    0 (  0)   30 ( 29) 
C 12035 13009 ac040109f1    913 (  0)  0.00 0.00 0.21    0 (  0)   36 ( 36) 
  12222 13181 eg030109r1    848 (  0)  1.32 0.00 0.11   49 ( 49)    3 (  3) 
  12226 13191 be080109r1    887 (  0)  0.22 0.00 0.11   50 ( 50)    0 (  0) 
  12307 13243 bf010109r1    743 (  0)  3.95 0.23 0.34   51 ( 51)    0 ( 10) 
  12573 13546 db100109r1    663 (  0)  0.97 1.10 0.00   48 ( 48)  202 (261) 
  12712 13652 be010109r1    848 (178)  1.01 0.00 0.11   46 ( 46)    1 ( 21) 
  12890 13862 bc080109r1    877 (368)  0.00 0.22 0.11   47 ( 47)    8 (  5) 
C 13088 14047 df030109f1    735 (448)  2.79 0.81 0.35    3 ( 33)   97 (148) 
  13158 14126 ag080109r1    782 (544)  1.42 1.75 0.11   53 ( 53)    2 ( 99) 
C 13175 14159 cd060109f1    898 (657)  1.12 0.30 0.20    0 ( 27)    0 ( 28) 
  13203 14193 bh060109r1    680 (528)  2.40 0.76 0.00   61 ( 93)  139 (139) 
  13220 14188 eb020109r1    747 (591)  1.66 0.83 0.00   61 ( 63)   64 (137) 
  13378 14323 ee080109f1    673 (722)  0.28 0.14 0.14   32 ( 32)  192 (192) 

Overall discrep rates (%):             1.51 0.31 0.08

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90   10765  76.0   10765  76.0    0.00
 89      49   0.3   10814  76.4    0.00
 88      88   0.6   10902  77.0    0.00
 87      55   0.4   10957  77.4    0.00
 86      43   0.3   11000  77.7    0.00
 85      44   0.3   11044  78.0    0.00
 84      42   0.3   11086  78.3    0.00
 83      47   0.3   11133  78.6    0.00
 82      45   0.3   11178  78.9    0.00
 81     108   0.8   11286  79.7    0.00
 80      32   0.2   11318  79.9    0.00
 79      27   0.2   11345  80.1    0.00
 78      24   0.2   11369  80.3    0.00
 77      31   0.2   11400  80.5    0.00
 76      61   0.4   11461  80.9    0.00
 75      35   0.2   11496  81.2    0.00
 74      30   0.2   11526  81.4    0.00
 73      13   0.1   11539  81.5    0.00
 72      10   0.1   11549  81.6    0.00
 71      15   0.1   11564  81.7    0.00
 70      28   0.2   11592  81.9    0.00
 69      20   0.1   11612  82.0    0.00
 68      15   0.1   11627  82.1    0.00
 67       7   0.0   11634  82.2    0.00
 66    1093   7.7   12727  89.9    0.00
 65      11   0.1   12738  90.0    0.00
 64      11   0.1   12749  90.0    0.00
 63       6   0.0   12755  90.1    0.00
 62       6   0.0   12761  90.1    0.00
 61     523   3.7   13284  93.8    0.00
 60      66   0.5   13350  94.3    0.00
 59       2   0.0   13352  94.3    0.00
 58      10   0.1   13362  94.4    0.00
 57       8   0.1   13370  94.4    0.00
 56      77   0.5   13447  95.0    0.00
 55     124   0.9   13571  95.8    0.00
 54      23   0.2   13594  96.0    0.00
 53     215   1.5   13809  97.5    0.00
 52      79   0.6   13888  98.1    0.00
 51      57   0.4   13945  98.5    0.00
 50      82   0.6   14027  99.1    0.00
 49      10   0.1   14037  99.1    0.00
 48       5   0.0   14042  99.2    0.00
 47       9   0.1   14051  99.2    0.00
 46       3   0.0   14054  99.3    0.00
 45      20   0.1   14074  99.4    0.01
 44       2   0.0   14076  99.4    0.01
 43       2   0.0   14078  99.4    0.01
 42       2   0.0   14080  99.4    0.01
 40      17   0.1   14097  99.6    0.01
 38       4   0.0   14101  99.6    0.01
 37       1   0.0   14102  99.6    0.01
 36       1   0.0   14103  99.6    0.01
 34       1   0.0   14104  99.6    0.01
 33       4   0.0   14108  99.6    0.01
 32       1   0.0   14109  99.6    0.01
 30       1   0.0   14110  99.7    0.01
 29       4   0.0   14114  99.7    0.02
 28       2   0.0   14116  99.7    0.02
 26       3   0.0   14119  99.7    0.03
 25       1   0.0   14120  99.7    0.03
 24       1   0.0   14121  99.7    0.04
 22       5   0.0   14126  99.8    0.07
 20       1   0.0   14127  99.8    0.08
 19       1   0.0   14128  99.8    0.09
 10       2   0.0   14130  99.8    0.29
 -1      29   0.2   14159 100.0   29.29   (quality -1 = terminal quality 0)

Avg. full length: 14159.0, trimmed (qual > -1): 14130.0
Avg. quality: 84.0 per base

Initial, terminal qual 0 segments:  1-2, 14133-14159

Regions of LLR- adjusted quality < 2.0:
1-2, 14123-14125, 14133-14159, 

3 regions, avg size 10.7, avg spacing 4719.7

First_start: 3, last_end: 14131
 Unused pair: ag120109f1 cd060109r1  -13.5   1
LLR breakdown: discreps: -1.3 (<20 part: -1.3 (#=14), >20:0.0 (#=0); in HQ: -0.3, out HQ -1.0), match: 3.0  trail: 0.0  lead: -16.0  total: -14.3  116  8.12 0.62 0.00  ag120109f1       36   195 (733)  C cd060109r1   (809)   212    52 *
 Unused pair: ag120109r1 eg070109r1  -6.9   0
LLR breakdown: discreps: -0.3 (<20 part: -0.3 (#=5), >20:0.0 (#=0); in HQ: 0.0, out HQ -0.3), match: 11.7  trail: -18.7  lead: 0.0  total: -7.3  509  0.94 0.00 0.00  ag120109r1       91   622 (305)  C eg070109r1   (1)   967   436 *
 Unused pair: ag120109r1 cd060109r1  -16.2   1
LLR breakdown: discreps: -1.3 (<20 part: -1.3 (#=14), >20:0.0 (#=0); in HQ: -0.3, out HQ -1.0), match: 3.0  trail: -18.7  lead: 0.0  total: -17.0  116  8.12 0.62 0.00  ag120109r1      463   622 (305)    cd060109r1       52   212 (809) *
 Unused pair: ag120109r1 cc030109f1  -6.0   0
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=0), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 12.6  trail: -18.7  lead: 0.0  total: -6.1  558  0.00 0.00 0.00  ag120109r1       56   622 (305)  C cc030109f1   (266)   701   135 *
 Unused pair: ag120109r1 bg040109f1  -6.0   0
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=0), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 12.6  trail: -18.7  lead: 0.0  total: -6.1  558  0.00 0.00 0.00  ag120109r1       56   622 (305)  C bg040109f1   (179)   762   196 *
 Unused pair: ag120109r1 bd020109f1  -6.5   0
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=2), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 12.1  trail: -18.7  total: -6.6  530  0.18 0.18 0.00  ag120109r1       78   622 (305)  C bd020109f1   (0)   946   401 *

Slack, # used pairs (max_score), unused
 0  1258  (20.4)     4 (-6.0)     4068
 1   674  (20.0)     2 (-13.5)      313
 2   179  (19.9)     0 ( 0.0)        3
 3    56  (17.8)     0 ( 0.0)        0
 4    44  (15.3)     0 ( 0.0)        0
 5    31  (17.6)     0 ( 0.0)        0
 6     6  (17.8)     0 ( 0.0)        0
 7     3  (13.0)     0 ( 0.0)        0
 8     3  ( 7.3)     0 ( 0.0)        0
 9     2  ( 3.9)     0 ( 0.0)        0
10     1  ( 3.9)     0 ( 0.0)        0
99     0  ( 0.0)  2121 ( 0.0)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -     0        0+
 5155 -  5398      244       dd080109r1   (4176)    No           1223
14132 - right       28+      ee080109f1   (13378)    No            781+

Bottom strand: 
 left -  1695     1695+      af100109r1   (2659)    No           2659+
12974 - 13090      117       df030109f1   (14047)    No           1074 
14160 - right        0+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  22976  22976 168417 (100.00)     7  0    0   0   0   0     0 (0.00)    0  3152 (1.87)
51  13340  36316 145441 ( 86.36)     2  0    0   0   0   0     0 (0.00)    0  3152 (2.17)
50   4535  40851 132101 ( 78.44)     0  0    0   0   0   0     0 (0.00)    0  3152 (2.39)
48    884  41735 127566 ( 75.74)     0  0    0   0   0   0     0 (0.00)    0  3152 (2.47)
47    654  42389 126682 ( 75.22)     0  0    0   0   0   0     0 (0.00)    0  3152 (2.49)
46   2695  45084 126028 ( 74.83)     2  0    0   0   0   0     0 (0.00)    0  3152 (2.50)
45   4783  49867 123333 ( 73.23)     3  0    0   0   0   0     0 (0.00)    0  3152 (2.56)
44   3857  53724 118550 ( 70.39)     1  0    0   0   0   0     0 (0.00)    0  3152 (2.66)
43   8667  62391 114693 ( 68.10)     0  0    0   0   0   0     0 (0.00)    0  3152 (2.75)
42  11126  73517 106026 ( 62.95)     4  0    0   0   0   0     0 (0.00)    0  3152 (2.97)
41   3281  76798  94900 ( 56.35)     0  0    0   0   0   0     0 (0.00)    0  3152 (3.32)
40  10666  87464  91619 ( 54.40)    21  0    0   0   0   0     0 (0.00)    0  3152 (3.44)
39   1053  88517  80953 ( 48.07)     0  0    0   0   0   0     0 (0.00)    0  3152 (3.89)
38   1627  90144  79900 ( 47.44)     1  0    0   0   0   0     0 (0.00)    0  3152 (3.94)
37   4203  94347  78273 ( 46.48)    11  0    0   0   0   0     0 (0.00)    0  3152 (4.03)
36    715  95062  74070 ( 43.98)     0  0    0   0   0   0     0 (0.00)    0  3152 (4.26)
35   6507 101569  73355 ( 43.56)    16  0    0   0   0   0     0 (0.00)    0  3152 (4.30)
34   1616 103185  66848 ( 39.69)    34  0    0   0   0   0     0 (0.00)    0  3152 (4.72)
33   2257 105442  65232 ( 38.73)    10  0    0   0   0   0     0 (0.00)    0  3152 (4.83)
32   2215 107657  62975 ( 37.39)    37  0    0   0   0   0     0 (0.00)    0  3152 (5.01)
31    973 108630  60760 ( 36.08)    12  0    0   0   1   0     1 (0.10)    1  3152 (5.19)
30   1180 109810  59787 ( 35.50)     7  0    0   0   0   0     0 (0.00)    1  3151 (5.27)
29   4092 113902  58607 ( 34.80)   109  0    0   3   2   0     5 (0.12)    6  3151 (5.38)
28   1228 115130  54515 ( 32.37)    16  0    0   0   1   0     1 (0.08)    7  3146 (5.77)
27   1896 117026  53287 ( 31.64)    62  0    0   1   0   0     1 (0.05)    8  3145 (5.90)
26    853 117879  51391 ( 30.51)    39  0    0   1   2   0     3 (0.35)   11  3144 (6.12)
25   2354 120233  50538 ( 30.01)    63  0    0   3   1   0     4 (0.17)   15  3141 (6.22)
24   1926 122159  48184 ( 28.61)    71  0    0   4   0   0     4 (0.21)   19  3137 (6.51)
23   1578 123737  46258 ( 27.47)    46  0    0   2   2   0     4 (0.25)   23  3133 (6.77)
22   1501 125238  44680 ( 26.53)   101  0    0   3   0   0     3 (0.20)   26  3129 (7.00)
21   1869 127107  43179 ( 25.64)    35  0    0   4   5   0     9 (0.48)   35  3126 (7.24)
20   1612 128719  41310 ( 24.53)    75  0    0   5   1   0     6 (0.37)   41  3117 (7.55)
19   2565 131284  39698 ( 23.57)   121  0    0  14   5   0    19 (0.74)   60  3111 (7.84)
18   1670 132954  37133 ( 22.05)    29  0    0   8   7   1    16 (0.96)   76  3092 (8.33)
17   1797 134751  35463 ( 21.06)    76  0    0  16   4   0    20 (1.11)   96  3076 (8.67)
16   1810 136561  33666 ( 19.99)   131  0    0  22  10   0    32 (1.77)  128  3056 (9.08)
15   2275 138836  31856 ( 18.91)    60  0    0  28  14   3    45 (1.98)  173  3024 (9.49)
14   2007 140843  29581 ( 17.56)    67  0    0  39   7   3    49 (2.44)  222  2979 (10.07)
13   2791 143634  27574 ( 16.37)    88  0    0  82  19   5   106 (3.80)  328  2930 (10.63)
12   2369 146003  24783 ( 14.72)    43  0    0  67  14   5    86 (3.63)  414  2824 (11.39)
11   3417 149420  22414 ( 13.31)    73  0    0 181  40  12   233 (6.82)  647  2738 (12.22)
10   4310 153730  18997 ( 11.28)   117  0    0 264  50  16   330 (7.66)  977  2505 (13.19)
 9   5743 159473  14687 (  8.72)   222  0    0 449  78  46   573 (9.98)  1550  2175 (14.81)
 8   3843 163316   8944 (  5.31)   164  0    0 375  61  16   452 (11.76)  2002  1602 (17.91)
 7   2928 166244   5101 (  3.03)   138  0    0 387  92  12   491 (16.77)  2493  1150 (22.54)
 6   1284 167528   2173 (  1.29)    64  0    0 196  66   8   270 (21.03)  2763  659 (30.33)
 4    556 168084    889 (  0.53)    38  0    0  48   8   0    56 (10.07)  2819  389 (43.76)
 0    333 168417    333 (  0.20)     6  0   326   0   7   0   333 (100.00)  3152  333 (100.00)
-1    147 168564      0 (  0.00)  13055  0    0  11  13   2    26 (17.69)  3178    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90 121926 121926 163935 (100.00)     0  0    0   0   0   0     0 (0.00)    0  2108 (1.29)
89    396 122322  42009 ( 25.63)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.02)
88    613 122935  41613 ( 25.38)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.07)
87    365 123300  41000 ( 25.01)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.14)
86    310 123610  40635 ( 24.79)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.19)
85    373 123983  40325 ( 24.60)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.23)
84    269 124252  39952 ( 24.37)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.28)
83    306 124558  39683 ( 24.21)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.31)
82    276 124834  39377 ( 24.02)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.35)
81    846 125680  39101 ( 23.85)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.39)
80    204 125884  38255 ( 23.34)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.51)
79    112 125996  38051 ( 23.21)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.54)
78    125 126121  37939 ( 23.14)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.56)
77    127 126248  37814 ( 23.07)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.57)
76    321 126569  37687 ( 22.99)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.59)
75    124 126693  37366 ( 22.79)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.64)
74     98 126791  37242 ( 22.72)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.66)
73    104 126895  37144 ( 22.66)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.68)
72     68 126963  37040 ( 22.59)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.69)
71    141 127104  36972 ( 22.55)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.70)
70    145 127249  36831 ( 22.47)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.72)
69    106 127355  36686 ( 22.38)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.75)
68     83 127438  36580 ( 22.31)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.76)
67     61 127499  36497 ( 22.26)     3  0    0   0   0   0     0 (0.00)    0  2108 (5.78)
66   9139 136638  36436 ( 22.23)     0  0    0   0   0   0     0 (0.00)    0  2108 (5.79)
65    144 136782  27297 ( 16.65)     0  0    0   0   0   0     0 (0.00)    0  2108 (7.72)
64     58 136840  27153 ( 16.56)     0  0    0   0   0   0     0 (0.00)    0  2108 (7.76)
63     18 136858  27095 ( 16.53)     0  0    0   0   0   0     0 (0.00)    0  2108 (7.78)
62     49 136907  27077 ( 16.52)     2  0    0   0   0   0     0 (0.00)    0  2108 (7.79)
61   4065 140972  27028 ( 16.49)     0  0    0   0   0   0     0 (0.00)    0  2108 (7.80)
60    428 141400  22963 ( 14.01)     2  0    0   0   0   0     0 (0.00)    0  2108 (9.18)
59    104 141504  22535 ( 13.75)     2  0    0   0   0   0     0 (0.00)    0  2108 (9.35)
58    101 141605  22431 ( 13.68)     2  0    0   0   0   0     0 (0.00)    0  2108 (9.40)
57    159 141764  22330 ( 13.62)     0  0    0   0   0   0     0 (0.00)    0  2108 (9.44)
56    448 142212  22171 ( 13.52)     2  0    0   0   0   0     0 (0.00)    0  2108 (9.51)
55    856 143068  21723 ( 13.25)     0  0    0   0   0   0     0 (0.00)    0  2108 (9.70)
54    354 143422  20867 ( 12.73)     2  0    0   0   0   0     0 (0.00)    0  2108 (10.10)
53   1397 144819  20513 ( 12.51)     0  0    0   0   0   0     0 (0.00)    0  2108 (10.28)
52    584 145403  19116 ( 11.66)     1  0    0   0   0   0     0 (0.00)    0  2108 (11.03)
51    374 145777  18532 ( 11.30)     3  0    0   0   0   0     0 (0.00)    0  2108 (11.37)
50    462 146239  18158 ( 11.08)     0  0    0   0   0   0     0 (0.00)    0  2108 (11.61)
49    185 146424  17696 ( 10.79)     2  0    0   0   0   0     0 (0.00)    0  2108 (11.91)
48    175 146599  17511 ( 10.68)     2  0    0   0   0   0     0 (0.00)    0  2108 (12.04)
47    179 146778  17336 ( 10.57)     2  0    0   0   0   0     0 (0.00)    0  2108 (12.16)
46    174 146952  17157 ( 10.47)     0  0    0   0   0   0     0 (0.00)    0  2108 (12.29)
45    242 147194  16983 ( 10.36)     0  0    0   0   0   0     0 (0.00)    0  2108 (12.41)
44    317 147511  16741 ( 10.21)     3  0    0   0   0   0     0 (0.00)    0  2108 (12.59)
43    182 147693  16424 ( 10.02)     0  0    0   0   0   0     0 (0.00)    0  2108 (12.83)
42    221 147914  16242 (  9.91)     0  0    0   0   0   0     0 (0.00)    0  2108 (12.98)
41    243 148157  16021 (  9.77)     0  0    0   0   0   0     0 (0.00)    0  2108 (13.16)
40   3573 151730  15778 (  9.62)     4  0    0   0   0   0     0 (0.00)    0  2108 (13.36)
39     92 151822  12205 (  7.45)     0  0    0   0   0   0     0 (0.00)    0  2108 (17.27)
38     35 151857  12113 (  7.39)     0  0    0   0   0   0     0 (0.00)    0  2108 (17.40)
37     59 151916  12078 (  7.37)     0  0    0   0   0   0     0 (0.00)    0  2108 (17.45)
36     38 151954  12019 (  7.33)     0  0    0   0   0   0     0 (0.00)    0  2108 (17.54)
35     61 152015  11981 (  7.31)     0  0    0   1   0   0     1 (1.64)    1  2108 (17.59)
34     89 152104  11920 (  7.27)     4  0    0   0   0   0     0 (0.00)    1  2107 (17.68)
33     98 152202  11831 (  7.22)     2  0    0   0   0   0     0 (0.00)    1  2107 (17.81)
32     89 152291  11733 (  7.16)     3  0    0   0   0   0     0 (0.00)    1  2107 (17.96)
31     73 152364  11644 (  7.10)     1  0    0   1   1   0     2 (2.74)    3  2107 (18.10)
30     41 152405  11571 (  7.06)     0  0    0   0   0   0     0 (0.00)    3  2105 (18.19)
29    162 152567  11530 (  7.03)     0  0    0   4   2   0     6 (3.70)    9  2105 (18.26)
28     38 152605  11368 (  6.93)     1  0    0   1   1   0     2 (5.26)   11  2099 (18.46)
27    144 152749  11330 (  6.91)     4  0    0   1   0   0     1 (0.69)   12  2097 (18.51)
26     69 152818  11186 (  6.82)     0  0    0   1   2   0     3 (4.35)   15  2096 (18.74)
25    631 153449  11117 (  6.78)     2  0    0   5   1   0     6 (0.95)   21  2093 (18.83)
24    173 153622  10486 (  6.40)     2  0    0   4   0   0     4 (2.31)   25  2087 (19.90)
23    115 153737  10313 (  6.29)     1  0    0   2   2   0     4 (3.48)   29  2083 (20.20)
22    102 153839  10198 (  6.22)     1  0    0   6   0   0     6 (5.88)   35  2079 (20.39)
21    153 153992  10096 (  6.16)     2  0    0   3   4   0     7 (4.58)   42  2073 (20.53)
20    131 154123   9943 (  6.07)     1  0    0   5   1   0     6 (4.58)   48  2066 (20.78)
19    329 154452   9812 (  5.99)     1  0    0  12   5   0    17 (5.17)   65  2060 (20.99)
18    115 154567   9483 (  5.78)     1  0    0   7   6   1    14 (12.17)   79  2043 (21.54)
17    206 154773   9368 (  5.71)     1  0    0  14   3   0    17 (8.25)   96  2029 (21.66)
16    347 155120   9162 (  5.59)     3  0    0  16   9   0    25 (7.20)  121  2012 (21.96)
15    286 155406   8815 (  5.38)     1  0    0  25  10   4    39 (13.64)  160  1987 (22.54)
14    311 155717   8529 (  5.20)     0  0    0  28   6   3    37 (11.90)  197  1948 (22.84)
13    600 156317   8218 (  5.01)     3  0    0  58  10   5    73 (12.17)  270  1911 (23.25)
12    496 156813   7618 (  4.65)     1  0    0  53  10   4    67 (13.51)  337  1838 (24.13)
11    889 157702   7122 (  4.34)     3  0    0 139  29  11   179 (20.13)  516  1771 (24.87)
10   1199 158901   6233 (  3.80)     4  0    0 188  35  13   236 (19.68)  752  1592 (25.54)
 9   1828 160729   5034 (  3.07)     1  0    0 288  43  35   366 (20.02)  1118  1356 (26.94)
 8   1144 161873   3206 (  1.96)     3  0    0 236  41  12   289 (25.26)  1407  990 (30.88)
 7   1124 162997   2062 (  1.26)     8  0    0 278  58  10   346 (30.78)  1753  701 (34.00)
 6    529 163526    938 (  0.57)     3  0    0 138  43   5   186 (35.16)  1939  355 (37.85)
 4    261 163787    409 (  0.25)     0  0    0  16   5   0    21 (8.05)  1960  169 (41.32)
 0    148 163935    148 (  0.09)     0  0   142   0   6   0   148 (100.00)  2108  148 (100.00)
-1   4629 168564      0 (  0.00)  15188  0   184 683 177  26   1070 (23.12)  3178    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0      29       29        2
 10       2       31        3
 19       1       32        3
 20       1       33        3
 22       5       38        4
 24       1       39        4
 25       1       40        4
 26       3       43        4
 28       2       45        4
 29       4       49        5
 30       1       50        6
 32       1       51        6
 33       4       55        5
 34       1       56        5
 36       1       57        5
 37       1       58        6
 38       4       62        7
 40      17       79        9
 42       2       81        9
 43       2       83        9
 44       2       85        9
 45      20      105       13
 46       3      108       13
 47       9      117       17
 48       5      122       20
 49      10      132       22
 50      82      214       40
 51      57      271       55
 52      79      350       79
 53     215      565      116
 54      23      588      117
 55     124      712      132
 56      77      789      127
 57       8      797      128
 58      10      807      127
 59       2      809      126
 60      66      875      130
 61     523     1398      166
 62       6     1404      168
 63       6     1410      170
 64      11     1421      169
 65      11     1432      173
 66    1093     2525       40
 67       7     2532       41
 68      15     2547       43
 69      20     2567       48
 70      28     2595       56
 71      15     2610       56
 72      10     2620       56
 73      13     2633       63
 74      30     2663       73
 75      35     2698       72
 76      61     2759       83
 77      31     2790       87
 78      24     2814       79
 79      27     2841       76
 80      32     2873       85
 81     108     2981       97
 82      45     3026      102
 83      47     3073      100
 84      42     3115      106
 85      44     3159      109
 86      43     3202      113
 87      55     3257      120
 88      88     3345      126
 89      49     3394      132
 90   10765    14159        1

SS region: 2084 (14.72%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
 4030     -5.0  [-2.9,  0.0]  (1, 1)
 4823     -3.4  [-3.4,  0.0]  (0, 1)
 5477     -3.2  [-3.2,  0.0]  (0, 1)
10649     -3.1  [-3.1,  0.0]  (0, 1)
11307     -3.4  [-3.4,  0.0]  (0, 1)
11876     -3.1  [-3.1,  0.0]  (0, 1)
12073     -3.7  [-2.1,  0.0]  (2, 0)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)  1540- 2452 [-3.1] (0,0)     ac010109f1         42-965 || local(+/-) (7.5,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -20.5 (<20 part: -20.5 (#=137), >20:0.0 (#=0); in HQ: -2.3, out HQ -18.2), match: 17.4  trail: 0.0  lead: 0.0  total: -3.1 
(0, 0)  3248- 4132 [-1.7] (0,0)   C ac010109r1         974-78 || local(+/-) (16.4,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -17.9 (<20 part: -17.9 (#=118), >20:0.0 (#=0); in HQ: 0.0, out HQ -17.9), match: 16.2  trail: 0.0  lead: 0.0  total: -1.7 
(0, 0)  7596- 7942 [-6.9] (0,0)   C cg120109r1         431-75 || local(+/-) (6.3,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -11.3 (<20 part: -11.3 (#=73), >20:0.0 (#=0); in HQ: 0.0, out HQ -11.3), match: 4.3  trail: 0.0  lead: 0.0  total: -7.0 
(0, 0) 11313-11879 [-3.3] (16,16)   C ag120109f1         602-36 || local(+/-) (12.7,12.9), distant (3.1,0.0)
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=0), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 12.6  trail: -16.0  lead: 0.0  total: -3.4 
(0, 0) 11313-11879 [-6.0] (16,16)     ag120109r1         56-622 || local(+/-) (12.7,12.9), distant (3.1,0.0)
LLR breakdown: discreps: 0.0 (<20 part: 0.0 (#=0), >20:0.0 (#=0); in HQ: 0.0, out HQ 0.0), match: 12.6  trail: -18.7  lead: 0.0  total: -6.1 
Bypassed: (0, 0) 11720-12306 [ 1.2] (0,0)     cd060109r1         52-643 || local(+/-) (8.4,0.0), distant (0.0,0.0)
(0, 0) 13091-13950 [14.5] (0,0)   C df030109f1         961-98 | 98 955 | DA:(932 955) || local(+/-) (16.1,0.0), distant (10.7,3.2)
(0, 0) 13281-14124 [16.8] (0,0)     eb020109r1         62-912 | 62 972 | DA:(914 972) || local(+/-) (18.0,0.0), distant (14.9,4.7)
(0, 0) 13410-14131 [15.6] (0,0)     ee080109f1         33-754 | 33 916 | DA:(755 916) || local(+/-) (15.9,0.0), distant (16.1,6.1)

Gaps in unique-read coverage:   E 13286- 14131

Contig 14.  244 reads; 13640 bp (untrimmed), 13530 (trimmed).
C     1   917 eg120109r1    840 (804)  0.12 0.12 0.00    0 (133)   49 ( 44) 
    111  1074 fc090109f1    898 (779)  0.75 0.11 0.11   23 ( 23)    2 (  2) 
    122  1045 fb120109f1    883 (773)  0.22 0.00 0.11   23 ( 23)    0 (  0) 
    132  1107 ee030109r1    895 (732)  0.54 0.11 0.00   51 ( 51)    2 (  7) 
C   135  1093 da050109r1    795 (679)  2.46 0.45 0.22   14 ( 89)   49 ( 49) 
    153  1095 be100109r1    829 (714)  1.13 0.11 0.34   51 ( 51)    4 ( 26) 
C   197  1165 ag090109r1    872 (687)  0.77 0.22 0.11    0 (  5)   54 ( 54) 
    224  1161 cd110109f1    866 (665)  0.33 0.22 0.33   30 ( 30)    3 (  2) 
    293  1232 cc110109f1    841 (584)  1.32 0.44 0.11   31 ( 57)    0 ( 37) 
    331  1267 ec110109r1    842 (550)  1.24 0.00 0.11   47 ( 47)    0 (  0) 
C   335  1315 ee060109r1    876 (546)  1.29 0.11 0.11    3 ( 17)   48 ( 48) 
    352  1281 ba070109f1    810 (539)  1.78 0.44 0.33   29 ( 29)    1 ( 60) 
    351  1297 dg080109f1    158 (198)  45.63 0.26 1.04  131 (244)   49 (602) 
C   372  1344 de080109f1    856 (518)  2.54 0.11 0.00    0 ( 43)   29 (100) 
C   439  1420 ee050109f1    731 (288)  2.55 1.04 0.23   91 (142)   29 ( 29) 
C   452  1394 ec020109f1    889 (475)  0.33 0.00 0.00    0 (  0)   26 ( 26) 
C   462  1458 bd040109r1    841 (393)  1.07 1.07 0.11    0 ( 70)   61 ( 61) 
C   483  1471 cd050109f1    805 (332)  2.02 1.06 0.32   17 ( 82)   33 ( 33) 
C   475  1418 eg020109r1    859 (438)  0.45 0.00 0.11    0 (  0)   48 ( 48) 
C   480  1463 ag060109r1    886 (423)  0.65 0.00 0.11    0 (  0)   55 (  7) 
C   490  1466 af030109f1    856 (379)  1.70 0.32 0.11    2 ( 44)   34 ( 34) 
C   512  1455 bh060109f1    753 (285)  1.90 0.12 0.36   71 (108)   32 ( 32) 
C   522  1463 ac120109r1    859 (409)  0.00 0.00 0.11    0 (  0)   55 (  7) 
    531  1540 ch050109r1    361 (189)  3.00 0.00 0.00   46 ( 46)  564 (564) 
    535  1486 bd070109f1    666 (200)  2.20 1.03 0.13   36 ( 41)  142 (220) 
    551  1514 ae020109r1    619 (179)  2.62 0.00 0.00   56 ( 56)  221 (272) 
C   580  1554 fc010109r1    795 (305)  1.38 0.34 0.11    0 (  0)  103 (114) 
C   604  1545 eb020109f1    837 (276)  0.55 0.99 0.00    0 (  0)   29 ( 29) 
    598  1547 ca010109r1    564 (274)  4.82 0.15 0.15   51 ( 51)  215 (268) 
    615  1615 eb060109f1    505 (291)  0.75 0.37 0.00   29 ( 29)  438 (458) 
    642  1629 ff080109r1    517 (245)  3.31 0.50 0.00   47 ( 47)  336 (408) 
C   717  1700 dc080109r1    871 (317)  0.96 0.21 0.00    0 (  0)   48 ( 48) 
C   719  1689 fe030109f1    908 (327)  0.00 0.00 0.11    0 (  0)   27 ( 27) 
C   724  1666 eb010109f1    822 (267)  1.86 0.11 0.11    0 (  0)   30 ( 54) 
C   823  1796 fc040109f1    883 (417)  0.53 0.32 0.11    0 (  0)   28 ( 28) 
C   934  1889 be050109f1    877 (531)  0.64 0.00 0.00    2 ( 20)   23 ( 23) 
C  1014  1981 cg040109f1    868 (600)  1.07 0.00 0.11    0 (  0)   32 ( 32) 
C  1043  2006 fg090109r1    840 (614)  1.10 0.22 0.00    2 (  2)   51 ( 51) 
C  1185  2145 ba040109r1    843 (755)  0.11 1.10 0.00    6 (  6)   50 ( 50) 
C  1280  2278 cg050109f1    723 (315)  2.13 1.18 0.24  127 (136)   27 ( 27) 
   1311  2264 ba050109r1    793 (751)  1.51 0.35 0.00   46 ( 46)   46 ( 78) 
C  1360  2278 bb110109f1    848 (313)  0.22 0.45 0.00    0 (  0)   30 ( 56) 
C  1463  2422 fg080109r1    859 (315)  0.77 0.22 0.11    0 (  0)   47 ( 47) 
C  1485  2446 aa030109r1    865 (313)  0.44 0.11 0.00    0 (  0)   57 ( 57) 
C  1546  2485 cd110109r1    722 (304)  3.17 1.25 0.23    7 (110)   51 ( 51) 
C  1634  2502 bf120109f1    738 (313)  1.80 0.72 0.12    9 ( 19)   28 ( 28) 
C  1753  2686 ed010109f1    872 (315)  0.22 0.22 0.00    0 ( 21)   29 ( 29) 
   1768  2759 ad050109r1    564 (290)  3.92 0.58 0.29   71 ( 71)  232 (353) 
   1774  2767 bc090109r1    679 (293)  2.12 1.74 0.00   47 ( 47)  144 (270) 
C  1827  2793 ff080109f1    898 (278)  0.43 0.21 0.00    1 (  1)   30 ( 30) 
C  1944  2893 bf100109r1    872 (170)  0.55 0.00 0.00    0 (  9)   47 ( 47) 
   2071  3031 ef030109f1    509 (  0)  9.23 0.64 0.26   32 ( 32)  149 (353) 
C  2187  3202 ba050109f1    371 (  0)  3.32 0.47 0.00  561 (595)   33 ( 33) 
   2263  3209 fg100109f1    887 ( 58)  0.44 0.11 0.11   29 ( 34)    0 (  0) 
   2302  3271 bb040109r1    905 (  0)  0.33 0.00 0.00   49 ( 49)    0 (  0) 
   2355  3319 fd070109r1    887 (  0)  0.65 0.11 0.11   45 ( 45)    1 (  9) 
   2355  3294 eb050109f1    869 ( 32)  0.44 0.33 0.22   29 ( 29)    2 (  2) 
   2566  3509 fb090109r1    872 (  0)  0.45 0.11 0.00   47 ( 47)    0 (  0) 
   2810  3759 de020109f1    889 (  0)  0.65 0.00 0.00   30 ( 30)    0 (  0) 
   2827  3760 be090109f1    890 (  0)  0.22 0.00 0.00   29 ( 29)    0 (  0) 
   2864  3805 aa010109f1    676 (  0)  5.48 1.23 0.34   29 ( 29)   19 (114) 
   2933  3830 bh120109f1    805 (  0)  1.50 0.35 0.00   30 ( 66)    3 (  3) 
   2960  3909 ff100109f1    902 (  0)  0.22 0.00 0.00   30 ( 30)    0 (  0) 
   3248  4224 ae070109r1    880 (  0)  0.54 0.11 0.22   53 ( 53)    1 ( 26) 
   3385  4351 fd080109r1    893 (111)  0.44 0.00 0.00   48 ( 48)    1 (  1) 
   3402  4310 eg010109f1    817 ( 40)  0.57 0.69 0.11   30 ( 30)    5 (  9) 
   3416  4389 af080109f1    898 (125)  0.64 0.00 0.21   36 ( 36)    0 (  0) 
   3479  4399 de120109f1    848 (155)  1.12 0.11 0.00   27 ( 50)    0 (  0) 
C  3490  4445 bb040109f1    802 (173)  2.07 0.44 0.66   10 ( 45)   30 ( 30) 
C  3560  4532 fd070109f1    914 (135)  0.21 0.11 0.11    1 (  0)   35 ( 31) 
C  3620  4599 ad050109f1    873 (  0)  1.26 0.74 0.11    0 ( 14)   29 ( 29) 
C  3668  4610 bc090109f1    893 (  0)  0.00 0.00 0.22    0 (  0)   32 ( 32) 
   3713  4683 fh070109r1    598 (134)  5.20 2.35 0.00   48 ( 48)  116 (321) 
C  3969  4914 fg100109r1    873 (173)  0.34 0.00 0.00    3 (  7)   48 ( 48) 
C  4038  4995 cg030109r1    660 (  0)  5.02 1.60 0.23   37 (171)   44 ( 42) 
   4044  4997 cg030109f1    839 ( 74)  0.23 0.23 0.11   30 ( 30)   53 ( 53) 
   4087  5056 ac070109f1    921 ( 36)  0.00 0.00 0.00   35 ( 35)    0 (  0) 
C  4187  5100 bh120109r1    788 (  0)  1.50 0.46 0.12    0 ( 39)   50 ( 61) 
   4196  5154 fb020109f1    912 (  0)  0.00 0.00 0.00   28 ( 28)    0 (  0) 
C  4288  5194 be090109r1    719 (  0)  1.50 0.13 0.50   60 ( 75)   49 ( 49) 
   4331  5246 ba120109r1    845 ( 83)  0.00 0.12 0.00   51 ( 51)    0 (  0) 
   4522  5487 ff060109r1    824 (  0)  2.19 0.11 0.22   47 ( 47)    4 ( 26) 
C  4542  5499 fb090109f1    899 (  0)  0.32 0.11 0.00    4 (  4)   25 ( 25) 
C  4561  5508 ca050109f1    871 (  0)  0.66 0.00 0.00    1 (  9)   39 ( 39) 
C  4640  5588 aa010109r1    854 (  0)  0.78 0.22 0.00    0 (  0)   52 ( 52) 
C  4670  5622 ff100109r1    873 (  0)  0.44 0.11 0.00    0 (  4)   51 ( 51) 
C  4673  5645 af080109r1    866 (  0)  1.20 0.00 0.11    1 (  1)   54 ( 54) 
C  4704  5678 fd080109f1    913 (  0)  0.53 0.00 0.00    8 (  6)   27 ( 27) 
C  4734  5688 fh070109f1    893 (  0)  0.65 0.00 0.00    4 (  4)   28 ( 28) 
C  4832  5811 ae070109f1    862 (  0)  1.80 0.53 0.00    0 ( 72)   38 ( 38) 
   5002  5947 aa110109r1    869 (  0)  0.34 0.00 0.00   56 ( 24)    2 (  2) 
   5008  5955 ba090109r1    830 (  0)  1.22 0.67 0.00   50 ( 18)    0 ( 27) 
   5063  5988 ee110109f1    703 (  0)  3.40 1.41 0.12   54 ( 54)   20 (117) 
C  5120  6070 de020109r1    527 (  0)  6.67 2.31 0.26  116 (310)   55 ( 55) 
   5264  6226 ff070109r1    877 (  0)  0.44 0.44 0.00   44 ( 44)    4 (  8) 
   5276  6247 da030109r1    591 (  0)  4.70 1.48 0.00   56 ( 67)  171 (284) 
C  5324  6283 fb020109r1    899 (  0)  0.00 0.00 0.00    0 (  0)   50 ( 50) 
   5474  6427 aa070109r1    858 (  0)  0.67 0.33 0.00   52 ( 52)    0 (  0) 
   5549  6475 fh020109r1    850 (  0)  0.34 0.11 0.00   49 ( 49)    1 (  1) 
C  5605  6511 ba120109f1    786 (  0)  1.29 0.59 0.00    0 (  0)   55 ( 67) 
   5634  6687 cb070109r1    442 (  0)  5.02 0.90 0.00   50 ( 61)  446 (475) 
C  5668  6650 ff060109f1    832 (  0)  2.65 0.21 0.21    4 (  1)   34 ( 34) 
   5680  6597 ea120109r1    836 (  0)  0.46 0.00 0.00   49 ( 49)    0 (  0) 
   5722  6655 eb070109r1    703 (  0)  1.72 0.98 0.37   49 ( 49)   71 (141) 
   5829  6795 ch080109f1    819 (  0)  2.15 0.54 0.11   37 ( 37)    0 ( 43) 
C  5890  6812 fc120109r1    550 (  0)  0.00 0.00 0.00  310 (308)   48 ( 48) 
   5898  6826 eh060109f1    870 (  0)  0.55 0.00 0.00   21 ( 21)    1 (  1) 
   5957  6921 ag040109f1    907 (  0)  0.11 0.00 0.00   34 ( 34)    3 (  3) 
C  6181  7152 ac070109r1    862 (  0)  0.65 0.54 0.11    0 (  0)   53 ( 53) 
   6180  7091 fc120109f1    550 (  0)  0.00 0.00 0.00   20 ( 18)  327 (327) 
C  6194  7137 ee110109r1    871 (  0)  0.11 0.00 0.00    0 (  0)   52 ( 52) 
C  6204  7105 eg010109r1    786 (  0)  1.52 0.35 0.12    0 ( 51)   46 ( 46) 
C  6234  7182 aa110109f1    865 (  0)  0.66 0.22 0.11    1 (  1)   36 ( 14) 
C  6244  7168 ba090109f1    872 (  0)  0.22 0.11 0.11    0 (  0)   22 (  3) 
   6254  7189 bb080109f1    878 (  0)  0.44 0.11 0.00   28 ( 27)    0 (  0) 
   6266  7199 bf040109f1    842 (  0)  1.43 0.11 0.22   25 ( 34)    0 ( 23) 
   6294  7233 bf030109f1    828 (  0)  1.66 0.22 0.22   30 ( 30)    5 (  5) 
   6310  7258 fd020109f1    898 (  0)  0.32 0.11 0.00   24 ( 24)    0 (  0) 
   6607  7520 ah010109f1    827 (  0)  1.26 0.00 0.00   36 ( 36)    3 (  8) 
C  6639  7603 aa070109f1    900 (  0)  0.54 0.00 0.00    0 (  0)   35 ( 35) 
C  6779  7712 fh020109f1    889 (  0)  0.11 0.00 0.00    0 (  0)   28 ( 28) 
   6902  7833 dd110109f1    173 (145)  12.39 2.02 0.58   19 ( 83)  566 (623) 
C  6955  7910 eh060109r1    871 (  0)  0.55 0.00 0.00    0 (  5)   54 ( 54) 
   6982  7929 dg010109r1    498 (  0)  1.12 0.00 0.00   49 ( 49)  365 (369) 
C  7088  8057 ag040109r1    892 (  0)  0.22 0.11 0.00    1 (  1)   53 ( 53) 
C  7125  8094 cb070109f1    915 (  0)  0.43 0.00 0.00    0 (  0)   29 ( 29) 
C  7191  8160 ff070109f1    391 (  0)  27.07 0.00 0.11    1 (289)   86 (152) 
C  7199  8222 ch080109r1    486 (  0)  3.63 0.86 0.00  392 (409)   53 ( 80) 
   7307  8271 ec050109r1    888 (  0)  0.65 0.00 0.11   47 ( 47)    0 (  0) 
C  7539  8510 bf030109r1    693 (  0)  4.93 0.35 0.23   72 ( 83)   48 ( 48) 
C  7759  8721 bb080109r1    897 (  0)  0.11 0.00 0.00    0 (  0)   50 ( 50) 
C  7857  8813 eb070109f1    887 (  0)  0.86 0.00 0.00    3 (  3)   29 ( 13) 
   7882  8813 fa010109r1    852 (  0)  0.45 0.11 0.00   50 ( 61)    0 (  0) 
C  7903  8811 ea120109f1    844 (  0)  0.45 0.23 0.11    1 (  1)   27 ( 11) 
   7947  8872 ef090109f1    861 (  0)  0.67 0.00 0.22   24 ( 24)    0 (  0) 
   7957  8860 ch120109r1    805 (  0)  1.17 0.23 0.00   47 ( 47)    0 (  0) 
   8033  8953 fh110109f1    873 (  0)  0.11 0.11 0.00   28 ( 28)    0 (  0) 
   8048  9033 ae050109f1    890 (  0)  1.17 0.11 0.00   35 ( 35)   12 ( 16) 
C  8232  9169 ec050109f1    880 (  0)  0.66 0.00 0.11    0 (  0)   26 ( 26) 
C  8238  9201 fd020109r1    895 (  0)  0.22 0.00 0.00    2 (  2)   52 ( 52) 
C  8234  9172 dd110109r1    387 (  0)  16.38 0.58 0.58   27 (160)   51 ( 51) 
C  8281  9248 dc070109r1    867 (  0)  0.98 0.43 0.00    0 ( 15)   48 ( 12) 
C  8281  9248 bf040109r1    905 (  0)  0.11 0.00 0.00    0 (  0)   50 ( 15) 
C  8477  9396 ah010109r1    847 (  0)  0.23 0.00 0.00    3 (  3)   56 ( 56) 
   8522  9514 ab050109r1    868 (  0)  1.20 0.11 0.11   74 ( 74)    0 (  0) 
   8683  9646 ah070109f1    897 (  0)  0.65 0.22 0.00   36 ( 36)    2 (  2) 
   8786  9693 eh100109r1    765 (  0)  1.58 0.36 0.12   49 ( 49)   35 ( 35) 
   8846  9812 aa040109r1    893 (  0)  0.33 0.00 0.00   60 ( 60)    0 (  0) 
   8893  9829 fg020109r1    878 (  0)  0.00 0.11 0.00   49 ( 49)    0 (  0) 
C  8910  9897 ce050109f1    923 (  0)  0.73 0.21 0.00    0 (  0)   30 ( 30) 
   8991  9900 fd120109r1    848 (  0)  0.12 0.00 0.12   47 ( 47)    1 (  1) 
   9016  9921 bh010109r1    848 (  0)  0.00 0.00 0.00   52 ( 52)    0 (  0) 
C  9135 10076 fa010109f1    887 (  0)  0.77 0.00 0.00    0 (  0)   28 ( 28) 
   9320 10250 fb110109f1    894 (  0)  0.22 0.00 0.00   28 ( 28)    0 (  0) 
C  9338 10255 ch120109f1    852 (  0)  0.79 0.23 0.00    0 (  0)   34 ( 54) 
C  9342 10294 ba030109r1    891 (  0)  0.33 0.00 0.00    1 (  1)   49 ( 49) 
   9351 10332 ab030109f1    908 (  0)  0.43 0.21 0.11   45 ( 45)    0 (  4) 
C  9521 10484 ah070109r1    893 (  0)  0.44 0.00 0.00    1 (  1)   54 ( 54) 
C  9539 10499 ef090109r1    886 (  0)  0.44 0.22 0.11    0 ( 13)   46 ( 46) 
C  9595 10586 ae050109r1    881 (  0)  0.85 0.32 0.32    2 (  2)   54 ( 54) 
   9685 10650 dg090109r1    817 (  0)  1.86 0.66 0.33   46 ( 46)    8 ( 29) 
   9748 10740 ce100109r1    531 (  0)  4.09 0.63 0.16   48 ( 80)  309 (354) 
   9833 10852 cg080109r1    466 (  0)  3.53 0.56 0.00   47 ( 61)  434 (434) 
   9856 10768 bg010109f1    861 (  0)  0.23 0.34 0.00   31 ( 54)    0 (  0) 
   9857 10827 ce030109r1    532 (  0)  4.09 0.63 0.16   45 ( 45)  291 (334) 
   9860 10814 aa090109r1    890 (  0)  0.22 0.00 0.00   55 ( 55)    0 (  4) 
   9899 10851 dh090109r1    764 (  0)  3.09 1.32 0.11   47 ( 58)    0 ( 98) 
C  9990 10882 bh010109f1    853 (  0)  0.46 0.00 0.11    0 (  0)   19 ( 27) 
  10098 11068 cf060109f1    891 (  0)  0.53 0.43 0.32   28 ( 28)    2 (  0) 
C 10117 11035 eh100109f1    640 (  0)  6.08 2.14 0.11    4 (268)   27 ( 27) 
C 10133 11054 fh110109r1    855 (  0)  0.57 0.00 0.11    0 (  0)   43 ( 42) 
  10138 11103 ab090109f1    901 (  0)  0.65 0.00 0.11   36 ( 36)    0 (  0) 
C 10270 11203 fg020109f1    903 (  0)  0.00 0.00 0.00    0 (  0)   25 ( 22) 
C 10315 11240 fd120109f1    879 (  0)  0.11 0.00 0.11    0 (  0)   30 ( 30) 
C 10322 11303 aa040109f1    889 (  0)  0.75 0.00 0.22    0 (  0)   52 ( 52) 
C 10473 11430 ce100109f1    847 (  0)  1.83 0.22 0.11    0 (  0)   30 ( 30) 
  10586 11544 ed080109r1    856 (  0)  0.88 0.11 0.00   47 ( 47)    3 (  8) 
C 10631 11619 ab030109r1    882 (  0)  0.22 0.00 0.11    0 (  0)   71 ( 67) 
C 10650 11572 fb110109r1    836 (  0)  0.46 0.11 0.00    0 (  0)   47 ( 47) 
  10761 11735 be060109r1    865 (  0)  0.65 0.11 0.11   50 ( 50)    1 ( 21) 
  10854 11823 af030109r1    811 (  0)  0.89 0.89 0.00   53 ( 53)   15 ( 46) 
C 10909 11862 dh090109f1    848 (  0)  0.76 0.22 0.22    0 (  0)   31 ( 31) 
C 10913 11842 dg120109r1    833 (  0)  0.68 0.00 0.00    0 (  0)   46 ( 50) 
C 10985 11954 ce030109f1    864 (  0)  0.96 0.00 0.00    0 (  0)   37 ( 51) 
  11018 11923 eg120109f1    702 (  0)  2.52 1.83 0.00   30 ( 30)    2 (131) 
  11047 12001 bh050109r1    830 (  0)  1.10 0.22 0.11   49 ( 49)    0 (  0) 
C 11057 12039 ab050109f1    852 (722)  0.63 0.95 0.11    0 (  0)   36 ( 40) 
  11172 12123 ec020109r1    826 (680)  1.12 0.11 0.00   51 ( 51)    5 ( 34) 
  11205 12148 eb100109f1    562 (538)  4.35 1.72 0.40   25 ( 48)  161 (237) 
  11273 12194 eg020109f1    749 (609)  3.12 0.78 0.11   21 ( 21)    3 ( 52) 
C 11280 12242 ab090109r1    864 (614)  0.33 0.11 0.00    0 (  0)   55 ( 55) 
C 11312 12270 aa090109f1    867 (591)  0.43 0.00 0.22    0 (  4)   35 ( 35) 
C 11317 12255 be080109f1    835 (550)  0.78 0.11 0.11   14 ( 31)   27 ( 25) 
  11353 12306 fc010109f1    867 (514)  0.65 0.11 0.00   31 ( 31)    0 (  9) 
  11434 12427 fg090109f1    125 (129)  15.50 2.63 0.29   29 ( 29)  623 (846) 
  11439 12434 cg050109r1    108 (108)  11.60 0.55 0.00   59 ( 59)  756 (795) 
  11445 12402 fg030109f1    885 (435)  0.22 0.11 0.00   30 ( 30)    0 (  0) 
C 11460 12394 eg030109f1    781 (372)  1.99 0.88 0.00    0 (  0)   30 ( 30) 
  11475 12416 ba040109f1    866 (413)  0.44 0.11 0.00   29 (  0)    0 (  7) 
  11475 12438 bd040109f1    834 (416)  2.03 0.32 0.00   29 (  1)    0 ( 17) 
  11479 12466 ee050109r1    843 (392)  1.60 0.32 0.11   50 ( 13)    1 ( 29) 
  11480 12453 ae030109r1    843 (382)  1.41 0.11 0.11   51 ( 15)    2 (  2) 
  11518 12445 aa120109r1    828 (354)  0.69 0.00 0.00   53 ( 53)    3 (  3) 
  11537 12509 de080109r1    638 (339)  6.68 0.47 0.12   47 ( 47)   73 (252) 
C 11649 12565 be010109f1    851 (272)  0.00 0.00 0.11    1 (  1)   26 ( 26) 
C 11668 12635 ae030109f1    819 (204)  1.50 0.11 0.64    0 ( 49)   35 ( 40) 
  11707 12685 ab070109r1    862 (166)  0.32 0.00 0.11   53 ( 21)    0 (  0) 
  11710 12670 bb070109r1    788 (134)  1.98 0.44 0.11   50 ( 17)    2 (  2) 
  11731 12703 ag090109f1    875 (160)  0.11 0.11 0.11   34 ( 34)    0 (  0) 
  11738 12636 bh110109r1    661 (134)  3.79 1.30 0.00   50 ( 50)    5 ( 83) 
C 11746 12667 bg010109r1    812 (171)  0.35 0.00 0.00    1 (  1)   54 ( 54) 
  11762 12687 bb110109r1    824 (122)  0.46 0.00 0.00   48 ( 48)    1 (  1) 
C 11763 12717 cg080109f1    842 (142)  0.65 0.11 0.32    1 (  1)   27 ( 27) 
  11772 12741 fg080109f1    862 (145)  0.43 0.21 0.21   31 ( 38)    0 (  0) 
C 11882 12799 bf010109f1    564 ( 89)  9.53 0.68 0.11    6 ( 50)   31 ( 52) 
  11944 12903 ee060109f1    870 (177)  0.22 0.00 0.00   30 ( 30)    1 (  1) 
C 11997 12940 ed080109f1    829 (190)  0.76 0.44 0.00    0 (  0)   28 ( 34) 
C 11994 12902 bc080109f1    725 (155)  2.43 0.35 0.35   17 ( 54)   28 ( 28) 
  12010 12955 ad120109f1    837 (222)  0.33 0.11 0.00   38 ( 38)    1 (  1) 
  12019 12991 fc040109r1    843 (239)  0.86 0.00 0.00   47 ( 47)    0 (  0) 
  12035 13026 cg040109r1    579 (131)  3.91 0.67 0.13   48 ( 60)  203 (261) 
C 12056 12988 bh050109f1    818 (228)  0.67 0.00 0.22    0 (  0)   31 ( 33) 
  12090 13104 ag060109f1    880 (361)  0.00 0.00 0.21   71 ( 71)    0 (  0) 
C 12111 13053 fg030109r1    827 (271)  0.45 0.11 0.00    0 (  0)   49 ( 49) 
  12176 13165 be050109r1    826 (378)  1.06 0.85 0.00   49 ( 49)    0 ( 34) 
C 12194 13152 ee080109r1    811 (369)  0.77 0.55 0.00    0 ( 13)   50 ( 50) 
  12277 13249 fe030109r1    862 (508)  0.54 0.00 0.00   49 ( 49)    0 (  0) 
C 12279 13222 be060109f1    832 (457)  0.87 0.22 0.00    0 (  0)   29 ( 29) 
  12376 13314 bf100109f1    853 (565)  0.55 0.00 0.00   28 ( 28)    0 (  9) 
C 12387 13312 eb100109r1    740 (525)  1.20 0.48 0.00   43 ( 45)   51 ( 51) 
  12403 13349 ac120109f1    833 (595)  0.44 0.33 0.00   43 ( 43)    0 (  0) 
  12427 13385 ec100109r1    855 (629)  0.33 0.00 0.00   48 ( 48)    1 (  1) 
  12470 13441 ac100109f1    873 (691)  0.43 0.32 0.00   35 ( 35)    3 (  7) 
  12478 13441 eb010109r1    834 (677)  0.77 0.66 0.00   50 ( 50)    0 (  0) 
  12489 13468 da100109f1    139 (142)  19.60 0.50 0.00  127 (262)  251 (314) 
C 12520 13487 ab070109f1    868 (708)  0.96 0.11 0.00    0 (  0)   34 ( 34) 
C 12545 13476 bb070109f1    431 (429)  13.28 0.84 0.72   71 (247)   25 ( 54) 
C 12545 13492 da040109r1    614 (610)  0.61 0.30 0.15  239 (239)   50 ( 50) 
  12572 13546 aa030109f1    892 (795)  0.43 0.00 0.00   44 ( 44)    2 (  6) 
C 12604 13525 aa120109f1    814 (744)  1.01 0.56 0.00    1 (  1)   32 ( 32) 
  12680 13596 bf120109r1    847 (804)  0.00 0.00 0.00   50 ( 50)    0 (  0) 
  12687 13640 ed010109r1    884 (795)  0.11 0.00 0.00   49 ( 49)    0 ( 23) 
C 12696 13658 ag080109f1    848 (787)  1.40 0.22 0.22    0 ( 41)   37 ( 41) 
  13189 14096 de110109f1     92 (100)  19.02 1.64 0.33   28 ( 28)  575 (714) 

Overall discrep rates (%):             1.69 0.31 0.09

Contig quality (quality, n_residues, %,  cum, cum %,  cum expected errs):
 90   12257  89.9   12257  89.9    0.00
 89      46   0.3   12303  90.2    0.00
 88      43   0.3   12346  90.5    0.00
 87      35   0.3   12381  90.8    0.00
 86      25   0.2   12406  91.0    0.00
 85      39   0.3   12445  91.2    0.00
 84      30   0.2   12475  91.5    0.00
 83      25   0.2   12500  91.6    0.00
 82      31   0.2   12531  91.9    0.00
 81      61   0.4   12592  92.3    0.00
 80      20   0.1   12612  92.5    0.00
 79      18   0.1   12630  92.6    0.00
 78      19   0.1   12649  92.7    0.00
 77      15   0.1   12664  92.8    0.00
 76      19   0.1   12683  93.0    0.00
 75      15   0.1   12698  93.1    0.00
 74      11   0.1   12709  93.2    0.00
 73       6   0.0   12715  93.2    0.00
 72      12   0.1   12727  93.3    0.00
 71      11   0.1   12738  93.4    0.00
 70      20   0.1   12758  93.5    0.00
 69      10   0.1   12768  93.6    0.00
 68      14   0.1   12782  93.7    0.00
 67       7   0.1   12789  93.8    0.00
 66     352   2.6   13141  96.3    0.00
 65       4   0.0   13145  96.4    0.00
 64       4   0.0   13149  96.4    0.00
 63       4   0.0   13153  96.4    0.00
 62       9   0.1   13162  96.5    0.00
 61     123   0.9   13285  97.4    0.00
 60       9   0.1   13294  97.5    0.00
 59       4   0.0   13298  97.5    0.00
 58       4   0.0   13302  97.5    0.00
 57       3   0.0   13305  97.5    0.00
 56      13   0.1   13318  97.6    0.00
 55      49   0.4   13367  98.0    0.00
 54       7   0.1   13374  98.0    0.00
 53      33   0.2   13407  98.3    0.00
 52      12   0.1   13419  98.4    0.00
 51      12   0.1   13431  98.5    0.00
 50       3   0.0   13434  98.5    0.00
 48       3   0.0   13437  98.5    0.00
 47       5   0.0   13442  98.5    0.00
 46       5   0.0   13447  98.6    0.00
 45       2   0.0   13449  98.6    0.00
 44       9   0.1   13458  98.7    0.00
 43       3   0.0   13461  98.7    0.00
 42       1   0.0   13462  98.7    0.00
 41       1   0.0   13463  98.7    0.00
 38       1   0.0   13464  98.7    0.00
 31       1   0.0   13465  98.7    0.00
 30       1   0.0   13466  98.7    0.00
 29       2   0.0   13468  98.7    0.01
 28       2   0.0   13470  98.8    0.01
 27       2   0.0   13472  98.8    0.01
 26       4   0.0   13476  98.8    0.02
 25       4   0.0   13480  98.8    0.04
 24       5   0.0   13485  98.9    0.06
 23       3   0.0   13488  98.9    0.07
 22       1   0.0   13489  98.9    0.08
 21       9   0.1   13498  99.0    0.15
 20       2   0.0   13500  99.0    0.17
 19       2   0.0   13502  99.0    0.19
 18       2   0.0   13504  99.0    0.23
 17       2   0.0   13506  99.0    0.27
 15       9   0.1   13515  99.1    0.55
 14       1   0.0   13516  99.1    0.59
 13       3   0.0   13519  99.1    0.74
 12       1   0.0   13520  99.1    0.80
 11       2   0.0   13522  99.1    0.96
 10       5   0.0   13527  99.2    1.46
  8       3   0.0   13530  99.2    1.94
 -1     110   0.8   13640 100.0  111.94   (quality -1 = terminal quality 0)

Avg. full length: 13640.0, trimmed (qual > -1): 13530.0
Avg. quality: 87.2 per base

Initial, terminal qual 0 segments:  1-88, 13619-13640

Regions of LLR- adjusted quality < 2.0:
1-88, 90, 92-93, 96-98, 100-101, 106-110, 115-117, 121-129, 
13614-13640, 

9 regions, avg size 15.6, avg spacing 1515.6

First_start: 134, last_end: 13617

Slack, # used pairs (max_score), unused
 0  1895  (20.4)     0 ( 0.0)     4362
 1  1187  (20.0)     0 ( 0.0)      332
 2   398  (20.0)     0 ( 0.0)        4
 3   131  (19.7)     0 ( 0.0)        0
 4    71  (17.5)     0 ( 0.0)        0
 5    25  (18.6)     0 ( 0.0)        0
 6     9  (17.9)     0 ( 0.0)        0
 7     4  (13.8)     0 ( 0.0)        0
 8     6  (13.5)     0 ( 0.0)        0
 9     1  (12.6)     0 ( 0.0)        0
10     1  ( 6.0)     0 ( 0.0)        0
85     0  ( 0.0)     1 (-9.4)        0
88     0  ( 0.0)     2 (-99.9)        0
90     0  ( 0.0)     1 (-98.4)        0
93     0  ( 0.0)     2 (-99.9)        0
94     0  ( 0.0)     1 (-9.4)        0
95     0  ( 0.0)     4 (-22.1)        0
96     0  ( 0.0)     1 (-99.9)        0
97     0  ( 0.0)     2 (-99.9)        0
98     0  ( 0.0)     3 (-9.4)        0
99     0  ( 0.0)   953 (16.3)        0

LLR histograms (used, unused pairs): 

   DS Gap         Size      Closest read (Start)   Covers   Read length required
                                                    now?        to cover
Top strand: 
 left -   133      133+
 1345 -  1356       12       ba050109r1   (1311)    Yes            46
13641 - right        0+      de110109f1   (13189)    No            451+

Bottom strand: 
 left -     0        0+      eg120109r1   ( 917)    No            917+
 3170 -  3499      330       bb040109f1   (4445)    No           1276 
13622 - right       19+

Read/contig alignment summary, by read base; trace qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
56  29998  29998 211944 (100.00)     8  0    0   1   0   0     1 (0.00)    1  4405 (2.08)
51  15554  45552 181946 ( 85.85)     2  0    0   0   0   0     0 (0.00)    1  4404 (2.42)
50   6243  51795 166392 ( 78.51)     0  0    0   0   0   0     0 (0.00)    1  4404 (2.65)
48   1038  52833 160149 ( 75.56)     0  0    0   0   0   0     0 (0.00)    1  4404 (2.75)
47    835  53668 159111 ( 75.07)     2  0    0   0   0   0     0 (0.00)    1  4404 (2.77)
46   3318  56986 158276 ( 74.68)     0  0    0   0   0   0     0 (0.00)    1  4404 (2.78)
45   6324  63310 154958 ( 73.11)     0  0    0   0   0   0     0 (0.00)    1  4404 (2.84)
44   4872  68182 148634 ( 70.13)     2  0    0   0   0   0     0 (0.00)    1  4404 (2.96)
43  10530  78712 143762 ( 67.83)     0  0    0   0   0   0     0 (0.00)    1  4404 (3.06)
42  14515  93227 133232 ( 62.86)    16  0    0   0   0   1     1 (0.01)    2  4404 (3.31)
41   4132  97359 118717 ( 56.01)     0  0    0   0   0   0     0 (0.00)    2  4403 (3.71)
40  13582 110941 114585 ( 54.06)    14  0    0   1   0   0     1 (0.01)    3  4403 (3.84)
39   1282 112223 101003 ( 47.66)     2  0    0   0   0   0     0 (0.00)    3  4402 (4.36)
38   1985 114208  99721 ( 47.05)     0  0    0   0   0   0     0 (0.00)    3  4402 (4.41)
37   5464 119672  97736 ( 46.11)     5  0    0   0   2   0     2 (0.04)    5  4402 (4.50)
36    854 120526  92272 ( 43.54)     3  0    0   0   0   0     0 (0.00)    5  4400 (4.77)
35   7712 128238  91418 ( 43.13)    21  0    0   0   0   0     0 (0.00)    5  4400 (4.81)
34   2077 130315  83706 ( 39.49)    28  0    0   0   0   0     0 (0.00)    5  4400 (5.26)
33   2720 133035  81629 ( 38.51)    29  0    0   0   0   0     0 (0.00)    5  4400 (5.39)
32   3121 136156  78909 ( 37.23)    35  0    0   0   0   0     0 (0.00)    5  4400 (5.58)
31   1129 137285  75788 ( 35.76)    13  0    0   0   0   0     0 (0.00)    5  4400 (5.81)
30   1443 138728  74659 ( 35.23)    13  0    0   1   0   0     1 (0.07)    6  4400 (5.89)
29   5013 143741  73216 ( 34.54)   163  0    0   2   0   0     2 (0.04)    8  4399 (6.01)
28   1473 145214  68203 ( 32.18)    24  0    0   0   1   0     1 (0.07)    9  4397 (6.45)
27   2299 147513  66730 ( 31.48)    59  0    0   2   0   0     2 (0.09)   11  4396 (6.59)
26   1135 148648  64431 ( 30.40)    55  0    0   3   1   0     4 (0.35)   15  4394 (6.82)
25   2915 151563  63296 ( 29.86)    80  0    0   2   1   0     3 (0.10)   18  4390 (6.94)
24   2447 154010  60381 ( 28.49)    71  0    0   6   0   0     6 (0.25)   24  4387 (7.27)
23   1897 155907  57934 ( 27.33)    51  0    0   4   0   0     4 (0.21)   28  4381 (7.56)
22   1816 157723  56037 ( 26.44)   122  0    0   3   6   0     9 (0.50)   37  4377 (7.81)
21   2184 159907  54221 ( 25.58)    56  0    0   7   2   1    10 (0.46)   47  4368 (8.06)
20   1984 161891  52037 ( 24.55)    75  0    0   9   4   0    13 (0.66)   60  4358 (8.37)
19   3017 164908  50053 ( 23.62)   155  0    0  15   3   2    20 (0.66)   80  4345 (8.68)
18   2064 166972  47036 ( 22.19)    44  0    0  18   1   0    19 (0.92)   99  4325 (9.20)
17   2092 169064  44972 ( 21.22)    94  0    0  18   6   2    26 (1.24)  125  4306 (9.57)
16   2246 171310  42880 ( 20.23)   175  0    0  34   6   2    42 (1.87)  167  4280 (9.98)
15   2865 174175  40634 ( 19.17)    98  0    0  43  14   4    61 (2.13)  228  4238 (10.43)
14   2374 176549  37769 ( 17.82)   106  0    0  61  12   5    78 (3.29)  306  4177 (11.06)
13   3245 179794  35395 ( 16.70)   159  0    0 104  14  11   129 (3.98)  435  4099 (11.58)
12   3170 182964  32150 ( 15.17)    89  0    0 108  26  12   146 (4.61)  581  3970 (12.35)
11   4387 187351  28980 ( 13.67)   164  0    0 248  42  11   301 (6.86)  882  3824 (13.20)
10   5351 192702  24593 ( 11.60)   235  0    0 326  72  22   420 (7.85)  1302  3523 (14.33)
 9   7347 200049  19242 (  9.08)   460  0    0 583 112  67   762 (10.37)  2064  3103 (16.13)
 8   4905 204954  11895 (  5.61)   290  0    0 510  96  21   627 (12.78)  2691  2341 (19.68)
 7   3939 208893   6990 (  3.30)   181  0    0 509 113  21   643 (16.32)  3334  1714 (24.52)
 6   1961 210854   3051 (  1.44)   145  0    0 354 101   6   461 (23.51)  3795  1071 (35.10)
 4    570 211424   1090 (  0.51)    43  0    0  74   8   1    83 (14.56)  3878  610 (55.96)
 0    520 211944    520 (  0.25)     3  0   515   0   5   7   527 (101.35)  4405  527 (101.35)
-1     38 211982      0 (  0.00)  17227  0    0   5   2   0     7 (18.42)  4412    0 (0.00)


Read/contig alignment summary, by read base; adjusted qualities
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)
90 170540 170540 205059 (100.00)     0  0    0   0   0   0     0 (0.00)    0  2650 (1.29)
89    484 171024  34519 ( 16.83)     0  0    0   0   0   0     0 (0.00)    0  2650 (7.68)
88    375 171399  34035 ( 16.60)     0  0    0   0   0   0     0 (0.00)    0  2650 (7.79)
87    293 171692  33660 ( 16.41)     0  0    0   0   0   0     0 (0.00)    0  2650 (7.87)
86    233 171925  33367 ( 16.27)     0  0    0   0   0   0     0 (0.00)    0  2650 (7.94)
85    376 172301  33134 ( 16.16)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.00)
84    270 172571  32758 ( 15.97)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.09)
83    228 172799  32488 ( 15.84)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.16)
82    263 173062  32260 ( 15.73)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.21)
81    835 173897  31997 ( 15.60)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.28)
80    163 174060  31162 ( 15.20)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.50)
79    133 174193  30999 ( 15.12)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.55)
78    105 174298  30866 ( 15.05)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.59)
77    115 174413  30761 ( 15.00)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.61)
76    218 174631  30646 ( 14.94)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.65)
75     98 174729  30428 ( 14.84)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.71)
74     57 174786  30330 ( 14.79)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.74)
73     87 174873  30273 ( 14.76)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.75)
72     59 174932  30186 ( 14.72)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.78)
71    110 175042  30127 ( 14.69)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.80)
70    153 175195  30017 ( 14.64)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.83)
69     64 175259  29864 ( 14.56)     0  0    0   0   0   0     0 (0.00)    0  2650 (8.87)
68     74 175333  29800 ( 14.53)     0  0    0   0   1   0     1 (1.35)    1  2650 (8.89)
67     66 175399  29726 ( 14.50)     0  0    0   0   0   0     0 (0.00)    1  2649 (8.91)
66   3861 179260  29660 ( 14.46)     0  0    0   3   0   1     4 (0.10)    5  2649 (8.93)
65    179 179439  25799 ( 12.58)     0  0    0   0   0   0     0 (0.00)    5  2645 (10.25)
64     45 179484  25620 ( 12.49)     0  0    0   0   1   0     1 (2.22)    6  2645 (10.32)
63     21 179505  25575 ( 12.47)     0  0    0   0   1   0     1 (4.76)    7  2644 (10.34)
62     77 179582  25554 ( 12.46)     0  0    0   0   0   0     0 (0.00)    7  2643 (10.34)
61   1261 180843  25477 ( 12.42)     0  0    0   0   0   0     0 (0.00)    7  2643 (10.37)
60    122 180965  24216 ( 11.81)     0  0    0   0   0   0     0 (0.00)    7  2643 (10.91)
59    139 181104  24094 ( 11.75)     0  0    0   0   0   0     0 (0.00)    7  2643 (10.97)
58    107 181211  23955 ( 11.68)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.03)
57    176 181387  23848 ( 11.63)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.08)
56    191 181578  23672 ( 11.54)     2  0    0   0   0   0     0 (0.00)    7  2643 (11.17)
55    461 182039  23481 ( 11.45)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.26)
54    343 182382  23020 ( 11.23)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.48)
53    436 182818  22677 ( 11.06)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.65)
52    267 183085  22241 ( 10.85)     0  0    0   0   0   0     0 (0.00)    7  2643 (11.88)
51    205 183290  21974 ( 10.72)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.03)
50    173 183463  21769 ( 10.62)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.14)
49    192 183655  21596 ( 10.53)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.24)
48    189 183844  21404 ( 10.44)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.35)
47    147 183991  21215 ( 10.35)     1  0    0   0   0   0     0 (0.00)    7  2643 (12.46)
46    201 184192  21068 ( 10.27)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.55)
45    231 184423  20867 ( 10.18)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.67)
44    383 184806  20636 ( 10.06)     0  0    0   0   0   0     0 (0.00)    7  2643 (12.81)
43    194 185000  20253 (  9.88)     0  0    0   0   0   0     0 (0.00)    7  2643 (13.05)
42    252 185252  20059 (  9.78)     6  0    0   0   0   1     1 (0.40)    8  2643 (13.18)
41    327 185579  19807 (  9.66)     0  0    0   0   0   0     0 (0.00)    8  2642 (13.34)
40   5066 190645  19480 (  9.50)     0  0    0   0   0   0     0 (0.00)    8  2642 (13.56)
39     32 190677  14414 (  7.03)     0  0    0   0   0   0     0 (0.00)    8  2642 (18.33)
38     23 190700  14382 (  7.01)     0  0    0   0   0   0     0 (0.00)    8  2642 (18.37)
37     40 190740  14359 (  7.00)     0  0    0   0   1   0     1 (2.50)    9  2642 (18.40)
36     52 190792  14319 (  6.98)     0  0    0   0   0   0     0 (0.00)    9  2641 (18.44)
35     79 190871  14267 (  6.96)     0  0    0   0   0   0     0 (0.00)    9  2641 (18.51)
34    109 190980  14188 (  6.92)     0  0    0   0   0   0     0 (0.00)    9  2641 (18.61)
33     78 191058  14079 (  6.87)     2  0    0   0   0   0     0 (0.00)    9  2641 (18.76)
32     73 191131  14001 (  6.83)     0  0    0   0   0   0     0 (0.00)    9  2641 (18.86)
31     53 191184  13928 (  6.79)     1  0    0   0   0   0     0 (0.00)    9  2641 (18.96)
30     34 191218  13875 (  6.77)     0  0    0   1   0   0     1 (2.94)   10  2641 (19.03)
29    147 191365  13841 (  6.75)     1  0    0   2   0   0     2 (1.36)   12  2640 (19.07)
28     26 191391  13694 (  6.68)     0  0    0   2   1   0     3 (11.54)   15  2638 (19.26)
27    142 191533  13668 (  6.67)     5  0    0   4   0   0     4 (2.82)   19  2635 (19.28)
26     73 191606  13526 (  6.60)     0  0    0   4   1   0     5 (6.85)   24  2631 (19.45)
25    371 191977  13453 (  6.56)     1  0    0   4   3   2     9 (2.43)   33  2626 (19.52)
24    184 192161  13082 (  6.38)     1  0    0   3   0   1     4 (2.17)   37  2617 (20.00)
23    146 192307  12898 (  6.29)     0  0    0   6   0   0     6 (4.11)   43  2613 (20.26)
22    102 192409  12752 (  6.22)     3  0    0   5   7   0    12 (11.76)   55  2607 (20.44)
21    166 192575  12650 (  6.17)     4  0    0   6   2   1     9 (5.42)   64  2595 (20.51)
20    182 192757  12484 (  6.09)     3  0    0   7   4   0    11 (6.04)   75  2586 (20.71)
19    296 193053  12302 (  6.00)     2  0    0  11   2   1    14 (4.73)   89  2575 (20.93)
18    134 193187  12006 (  5.85)     0  0    0   8   1   0     9 (6.72)   98  2561 (21.33)
17    235 193422  11872 (  5.79)     0  0    0  15   4   2    21 (8.94)  119  2552 (21.50)
16    328 193750  11637 (  5.67)     1  0    0  26   6   2    34 (10.37)  153  2531 (21.75)
15    430 194180  11309 (  5.51)     1  0    0  39  11   3    53 (12.33)  206  2497 (22.08)
14    399 194579  10879 (  5.31)     2  0    0  43   8   5    56 (14.04)  262  2444 (22.47)
13    676 195255  10480 (  5.11)     2  0    0  68   9   7    84 (12.43)  346  2388 (22.79)
12    628 195883   9804 (  4.78)     0  0    0  65  12   9    86 (13.69)  432  2304 (23.50)
11   1090 196973   9176 (  4.47)     0  0    0 155  23   8   186 (17.06)  618  2218 (24.17)
10   1360 198333   8086 (  3.94)     0  0    0 183  43  14   240 (17.65)  858  2032 (25.13)
 9   2264 200597   6726 (  3.28)     6  0    0 320  59  49   428 (18.90)  1286  1792 (26.64)
 8   1511 202108   4462 (  2.18)     8  0    0 305  62  13   380 (25.15)  1666  1364 (30.57)
 7   1603 203711   2951 (  1.44)     9  0    0 373  86  19   478 (29.82)  2144  984 (33.34)
 6    872 204583   1348 (  0.66)     5  0    0 229  59   5   293 (33.60)  2437  506 (37.54)
 4    300 204883    476 (  0.23)     0  0    0  30   6   0    36 (12.00)  2473  213 (44.75)
 0    176 205059    176 (  0.09)     0  0   172   0   4   1   177 (100.57)  2650  177 (100.57)
-1   6923 211982      0 (  0.00)  20551  0   343 1134 233  52   1762 (25.45)  4412    0 (0.00)


Depth 0 regions:

Block histogram:
Qual   bases    cum    blocks
  0     110      110        2
  8       3      113        3
 10       5      118        5
 11       2      120        6
 12       1      121        6
 13       3      124        7
 14       1      125        6
 15       9      134        7
 17       2      136        9
 18       2      138        9
 19       2      140        9
 20       2      142        8
 21       9      151        6
 22       1      152        5
 23       3      155        7
 24       5      160        7
 25       4      164        8
 26       4      168        7
 27       2      170        5
 28       2      172        4
 29       2      174        4
 30       1      175        4
 31       1      176        4
 38       1      177        4
 41       1      178        4
 42       1      179        5
 43       3      182        5
 44       9      191        7
 45       2      193        7
 46       5      198        9
 47       5      203        8
 48       3      206       10
 50       3      209       11
 51      12      221       15
 52      12      233       20
 53      33      266       26
 54       7      273       27
 55      49      322       34
 56      13      335       32
 57       3      338       31
 58       4      342       33
 59       4      346       34
 60       9      355       31
 61     123      478       46
 62       9      487       47
 63       4      491       48
 64       4      495       49
 65       4      499       48
 66     352      851       23
 67       7      858       26
 68      14      872       28
 69      10      882       31
 70      20      902       38
 71      11      913       38
 72      12      925       40
 73       6      931       42
 74      11      942       41
 75      15      957       42
 76      19      976       44
 77      15      991       48
 78      19     1010       51
 79      18     1028       54
 80      20     1048       58
 81      61     1109       62
 82      31     1140       66
 83      25     1165       68
 84      30     1195       74
 85      39     1234       81
 86      25     1259       84
 87      35     1294       84
 88      43     1337       97
 89      46     1383      103
 90   12257    13640        1

SS region: 494 (3.62%), flagged: 0 (0.00%)

Sites with total LLR scores < -3.0  [max pos LLR read, max neg LLR read]  (#discrep top reads, #discrep bottom reads):
  640     -4.2  [-4.2,  0.0]  (1, 0)
 1143     -3.6  [-2.0,  0.0]  (2, 0)
 1409     -3.6  [-3.6,  0.0]  (0, 1)
 1517     -3.5  [-3.5,  0.0]  (0, 1)
 1688    -12.0  [-5.6,  0.0]  (0, 3)
 2096     -3.3  [-3.3,  0.0]  (0, 1)
 2658     -3.7  [-3.7,  0.0]  (0, 1)
 4416     -3.1  [-3.1,  0.0]  (0, 1)
 5146     -4.2  [-4.2,  0.0]  (0, 1)
 8066     -3.1  [-3.1,  0.0]  (0, 1)
11009     -3.5  [-3.5,  0.0]  (0, 1)
11211     -3.4  [-3.4,  0.0]  (0, 1)
11252     -3.1  [-3.1,  0.0]  (0, 1)
11680     -3.7  [-2.1,  0.0]  (1, 1)
11847     -3.7  [-3.7,  0.0]  (0, 1)
12654     -3.7  [-2.1,  0.0]  (1, 1)
12875     -3.1  [-3.1,  0.0]  (0, 1)
13329     -3.7  [-3.7,  0.0]  (0, 1)

Read/contig discrepancies (* = higher-quality): None.
0 lower quality discrepant sites.

Reads with neg LLR score, or confirmed or high-qual unaligned seg > 20 bases, or other problem:

(Lngths init HQ, CF unalgn segs); aligned contig pos [LLR score]; (terminal HQ, CF unalgn); read id; aligned read pos
| confirmed read segments | unaligned read segments matching elsewhere
 (LU = local unaligned, DU = distant unaligned, DA = distant aligned, ** = overlaps trimmed region
 || Best local and distant LLR scores
(0, 0)     1-  868 [17.1] (0,5)   C eg120109r1         918-50 | 45 917 | DA:(**786 917**) || local(+/-) (16.3,0.0), distant (16.3,5.3)
(0, 0)  6921- 7267 [-8.8] (0,0)     dd110109f1         20-371 | 20 371  (504 934) | DA:(504 934) CHIMERIC || local(+/-) (1.8,0.0), distant (6.3,0.0)
LLR breakdown: discreps: -14.0 (<20 part: -14.0 (#=52), >20:0.0 (#=0); in HQ: -4.7, out HQ -9.3), match: 5.2  trail: 0.0  lead: 0.0  total: -8.8 
(0, 0)  8261- 9121 [-5.6] (0,0)   C dd110109r1         912-52 || local(+/-) (15.6,0.0), distant (0.0,0.0)
LLR breakdown: discreps: -19.4 (<20 part: -19.4 (#=151), >20:0.0 (#=0); in HQ: 0.0, out HQ -19.4), match: 13.7  trail: 0.0  lead: 0.0  total: -5.7 
(0, 0) 11463-11804 [-2.5] (0,0)     fg090109f1         30-379 || local(+/-) (6.4,0.0), distant (6.4,0.0)
LLR breakdown: discreps: -7.1 (<20 part: -7.1 (#=63), >20:0.0 (#=0); in HQ: -0.6, out HQ -6.5), match: 4.6  trail: 0.0  lead: 0.0  total: -2.5 
(0, 0) 12616-13217 [-2.6] (0,0)     da100109f1         128-732 || local(+/-) (5.3,0.0), distant (5.3,0.0)
LLR breakdown: discreps: -10.2 (<20 part: -10.2 (#=121), >20:0.0 (#=0); in HQ: -2.5, out HQ -7.7), match: 7.5  trail: 0.0  lead: 0.0  total: -2.7 
(1, 0) 13217-13521 [-4.2] (0,0)     de110109f1         29-337 || local(+/-) (3.2,0.0), distant (3.8,0.0)
LLR breakdown: discreps: -6.2 (<20 part: -6.2 (#=64), >20:0.0 (#=0); in HQ: -0.8, out HQ -5.4), match: 3.1  trail: 0.0  lead: -1.1  total: -4.2 

Gaps in unique-read coverage:   S 134- 2102, E 12766- 13617

Subclone/read contig links and consistency checks (* = inconsistency; Contig 0 = singletons)
Max subclone size: 5000

Size histogram for consistent forward-reverse pairs (*** = inconsistent pairs)
  ***     0

 Consistent opp sense links (* = not used in chain, ** = multiple non-zero):