Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/0.5X_med_error_no_variance/alignment/0.5X_med_error_no_variance.sorted.bam -nw 400 -hm 3

Alignment

Command line: bwa mem -t 32 ../data/GCF_000002285.3_CanFam3.1_genomic.fna.gz results/0.5X_med_error_no_variance/0.5X_med_error_no_variance_R1.fa results/0.5X_med_error_no_variance/0.5X_med_error_no_variance_R2.fa
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: bwa (0.7.19-r1273)
Analysis date: Wed Jul 30 17:41:58 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/0.5X_med_error_no_variance/alignment/0.5X_med_error_no_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 8,036,542
Mapped reads 8,036,542 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 8,036,542 / 100%
Mapped reads, first in pair 4,018,271 / 50%
Mapped reads, second in pair 4,018,271 / 50%
Mapped reads, both in pair 8,036,542 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Supplementary alignments 1 / 0%
Read min/max/mean length 57 / 150 / 150
Duplicated reads (estimated) 13,574 / 0.17%
Duplication rate 0.17%
Clipped reads 19,253 / 0.24%

ACGT Content

Number/percentage of A's 353,841,346 / 29.35%
Number/percentage of C's 249,888,867 / 20.73%
Number/percentage of T's 352,825,446 / 29.27%
Number/percentage of G's 248,838,940 / 20.64%
Number/percentage of N's 2,187 / 0%
GC Percentage 41.37%

Coverage

Mean 0.5
Standard Deviation 0.7184

Mapping Quality

Mean Mapping Quality 32.22

Insert size

Mean 368.79
Standard Deviation 25,975.55
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 1%
Mismatches 12,016,526
Insertions 225
Mapped reads with at least one insertion 0%
Deletions 189
Mapped reads with at least one deletion 0%
Homopolymer indels 27.29%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 61400564 0.5005 0.7171
NC_006584.3 85426708 42861466 0.5017 0.72
NC_006585.3 91889043 45991973 0.5005 0.7188
NC_006586.3 88276631 44194623 0.5006 0.7184
NC_006587.3 88915250 44482136 0.5003 0.7182
NC_006588.3 77573801 38800924 0.5002 0.7186
NC_006589.3 80974532 40506884 0.5002 0.7167
NC_006590.3 74330416 37178349 0.5002 0.7181
NC_006591.3 61074082 30621031 0.5014 0.7204
NC_006592.3 69331447 34659444 0.4999 0.7178
NC_006593.3 74389097 37190216 0.4999 0.7165
NC_006594.3 72498081 36230542 0.4997 0.7168
NC_006595.3 63241923 31611980 0.4999 0.7157
NC_006596.3 60966679 30499043 0.5003 0.7192
NC_006597.3 64190966 32088394 0.4999 0.7169
NC_006598.3 59632846 29857794 0.5007 0.7174
NC_006599.3 64289059 32154272 0.5002 0.7167
NC_006600.3 55844845 27945221 0.5004 0.7188
NC_006601.3 53741614 26871583 0.5 0.7171
NC_006602.3 58134056 29066686 0.5 0.7187
NC_006603.3 50858623 25421515 0.4998 0.719
NC_006604.3 61439934 30710805 0.4999 0.7178
NC_006605.3 52294480 26137194 0.4998 0.718
NC_006606.3 47698779 23840742 0.4998 0.7165
NC_006607.3 51628933 25806199 0.4998 0.7174
NC_006608.3 38964690 19476048 0.4998 0.7169
NC_006609.3 45876710 22925571 0.4997 0.7168
NC_006610.3 41182112 20582682 0.4998 0.7168
NC_006611.3 41845238 20910603 0.4997 0.7163
NC_006612.3 40214260 20105779 0.5 0.7166
NC_006613.3 39895921 19937612 0.4997 0.7175
NC_006614.3 38810281 19398099 0.4998 0.7187
NC_006615.3 31377067 15685065 0.4999 0.7142
NC_006616.3 42124431 21045753 0.4996 0.7157
NC_006617.3 26524999 13260001 0.4999 0.7164
NC_006618.3 30810995 15405747 0.5 0.7191
NC_006619.3 30902991 15451317 0.5 0.716
NC_006620.3 23914537 11956831 0.5 0.7181
NC_006621.3 123869142 61916875 0.4999 0.7171
NW_003726127.1 2660953 1334247 0.5014 0.7245
NW_003726128.1 1881673 936510 0.4977 0.7379
NW_003726129.1 1415205 717522 0.507 0.7387
NW_003726130.1 1067467 537271 0.5033 0.7443
NW_003726131.1 866315 433766 0.5007 0.7221
NW_003726132.1 881102 445157 0.5052 0.7368
NW_003726133.1 822601 409167 0.4974 0.73
NW_003726134.1 741967 373484 0.5034 0.7288
NW_003726135.1 745551 372872 0.5001 0.742
NW_003726136.1 602611 301153 0.4997 0.7141
NW_003726137.1 573630 285286 0.4973 0.7245
NW_003726138.1 666183 335377 0.5034 0.754
NW_003726139.1 557017 281974 0.5062 0.7477
NW_003726140.1 510604 257671 0.5046 0.7222
NW_003726141.1 497093 248072 0.499 0.7291
NW_003726142.1 492630 241188 0.4896 0.733
NW_003726143.1 577062 288586 0.5001 0.7633
NW_003726144.1 561270 280769 0.5002 0.7514
NW_003726145.1 407330 202186 0.4964 0.7154
NW_003726146.1 405216 201297 0.4968 0.703
NW_003726147.1 508668 249718 0.4909 0.7734
NW_003726148.1 540093 275090 0.5093 0.7835
NW_003726149.1 448434 227081 0.5064 0.7572
NW_003726150.1 377800 191694 0.5074 0.7279
NW_003726151.1 384880 193188 0.5019 0.7238
NW_003726152.1 367143 183586 0.5 0.7262
NW_003726153.1 399987 199191 0.498 0.7464
NW_003726154.1 376204 189581 0.5039 0.74
NW_003726155.1 416178 210883 0.5067 0.7557
NW_003726156.1 365470 184037 0.5036 0.7419
NW_003726157.1 322752 160180 0.4963 0.7145
NW_003726158.1 320591 165280 0.5155 0.7273
NW_003726159.1 310270 154795 0.4989 0.7385
NW_003726160.1 433650 209986 0.4842 0.7786
NW_003726161.1 273228 137390 0.5028 0.7158
NW_003726162.1 281659 139185 0.4942 0.7496
NW_003726163.1 320442 159900 0.499 0.7427
NW_003726164.1 265648 136492 0.5138 0.7409
NW_003726165.1 241365 123281 0.5108 0.734
NW_003726166.1 234529 121500 0.5181 0.7247
NW_003726167.1 252720 125692 0.4974 0.7287
NW_003726168.1 254975 128070 0.5023 0.7297
NW_003726169.1 226053 113387 0.5016 0.709
NW_003726170.1 223744 116085 0.5188 0.7047
NW_003726171.1 227140 113700 0.5006 0.7297
NW_003726172.1 219672 109495 0.4984 0.7304
NW_003726173.1 214597 110388 0.5144 0.7444
NW_003726174.1 386314 191697 0.4962 0.8448
NW_003726175.1 204342 102296 0.5006 0.7121
NW_003726176.1 201724 103788 0.5145 0.7322
NW_003726177.1 216332 111286 0.5144 0.7327
NW_003726178.1 200877 102293 0.5092 0.7357
NW_003726179.1 310654 150292 0.4838 0.7926
NW_003726180.1 200932 100200 0.4987 0.7181
NW_003726181.1 201410 99600 0.4945 0.7098
NW_003726182.1 292533 140993 0.482 0.7709
NW_003726183.1 192561 97195 0.5047 0.7204
NW_003726184.1 210134 107090 0.5096 0.7465
NW_003726185.1 197844 99290 0.5019 0.7414
NW_003726186.1 196813 102600 0.5213 0.7516
NW_003726187.1 180359 88495 0.4907 0.6831
NW_003726188.1 210247 100799 0.4794 0.7584
NW_003726189.1 177735 92688 0.5215 0.7563
NW_003726190.1 172100 87882 0.5106 0.7099
NW_003726191.1 166866 82195 0.4926 0.7075
NW_003726192.1 164926 88485 0.5365 0.7343
NW_003726193.1 157598 79195 0.5025 0.7234
NW_003726194.1 143980 71991 0.5 0.7191
NW_003726195.1 141074 71689 0.5082 0.7406
NW_003726196.1 139526 69900 0.501 0.7075
NW_003726197.1 142260 71977 0.506 0.7205
NW_003726198.1 138160 71400 0.5168 0.7639
NW_003726199.1 142296 74700 0.525 0.7223
NW_003726200.1 133119 66150 0.4969 0.7149
NW_003726201.1 129748 65097 0.5017 0.7449
NW_003726202.1 125962 64800 0.5144 0.735
NW_003726203.1 127429 63891 0.5014 0.7129
NW_003726204.1 128261 65991 0.5145 0.7471
NW_003726205.1 131872 66298 0.5027 0.7557
NW_003726206.1 133432 67489 0.5058 0.7688
NW_003726207.1 119670 59400 0.4964 0.7387
NW_003726208.1 144750 68693 0.4746 0.695
NW_003726209.1 120779 60600 0.5017 0.7077
NW_003726210.1 115952 58497 0.5045 0.7245
NW_003726211.1 118237 59400 0.5024 0.7235
NW_003726212.1 111908 55800 0.4986 0.7237
NW_003726213.1 117332 63590 0.542 0.7944
NW_003726214.1 111759 55800 0.4993 0.7174
NW_003726215.1 108801 51600 0.4743 0.7102
NW_003726216.1 112014 57000 0.5089 0.7807
NW_003726217.1 106428 51300 0.482 0.6971
NW_003726218.1 104912 54300 0.5176 0.7343
NW_003726219.1 104646 51900 0.496 0.7082
NW_003726220.1 103248 52197 0.5055 0.7465
NW_003726221.1 129482 65394 0.505 0.7617
NW_003726222.1 118473 61494 0.5191 0.7856
NW_003726223.1 99993 47100 0.471 0.7038
NW_003726224.1 109585 54000 0.4928 0.7465
NW_003726225.1 124049 61200 0.4934 0.7564
NW_003726226.1 99658 50393 0.5057 0.7106
NW_003726227.1 101741 51600 0.5072 0.7326
NW_003726228.1 97365 46196 0.4745 0.71
NW_003726229.1 94395 47700 0.5053 0.7213
NW_003726230.1 102992 49800 0.4835 0.7162
NW_003726231.1 95509 44697 0.468 0.678
NW_003726232.1 92047 45000 0.4889 0.7111
NW_003726233.1 87753 45596 0.5196 0.7054
NW_003726234.1 96536 47091 0.4878 0.7347
NW_003726235.1 86544 41100 0.4749 0.6569
NW_003726236.1 85476 42596 0.4983 0.6869
NW_003726237.1 110512 55194 0.4994 0.7801
NW_003726238.1 83291 42000 0.5043 0.6966
NW_003726239.1 82459 41700 0.5057 0.7099
NW_003726240.1 81605 43481 0.5328 0.737
NW_003726241.1 82380 40800 0.4953 0.6854
NW_003726242.1 102198 50091 0.4901 0.7397
NW_003726243.1 82108 41395 0.5042 0.7026
NW_003726244.1 87041 47700 0.548 0.7338
NW_003726245.1 79722 38992 0.4891 0.6798
NW_003726246.1 230124 111896 0.4862 0.9997
NW_003726247.1 78357 38995 0.4977 0.7151
NW_003726248.1 256406 124495 0.4855 1.0458
NW_003726249.1 78050 40200 0.5151 0.7363
NW_003726250.1 81930 39900 0.487 0.7183
NW_003726251.1 77100 37796 0.4902 0.7102
NW_003726252.1 77130 38095 0.4939 0.7008
NW_003726253.1 79078 41096 0.5197 0.7518
NW_003726254.1 90550 45295 0.5002 0.7722
NW_003726255.1 82767 42293 0.511 0.7083
NW_003726256.1 89070 40493 0.4546 0.7186
NW_003726257.1 97802 49796 0.5092 0.7892
NW_003726258.1 79712 39899 0.5005 0.7045
NW_003726259.1 79581 42290 0.5314 0.8044
NW_003726260.1 73720 36900 0.5005 0.7337
NW_003726261.1 97799 45300 0.4632 0.7324
NW_003726262.1 73171 37800 0.5166 0.7251
NW_003726263.1 104732 54292 0.5184 0.7974
NW_003726264.1 78935 37500 0.4751 0.6923
NW_003726265.1 72992 38095 0.5219 0.7169
NW_003726266.1 68721 35100 0.5108 0.7237
NW_003726267.1 73611 36286 0.4929 0.711
NW_003726268.1 68272 34200 0.5009 0.7102
NW_003726269.1 79297 39300 0.4956 0.713
NW_003726270.1 84443 42288 0.5008 0.7806
NW_003726271.1 80679 41995 0.5205 0.7521
NW_003726272.1 68834 34200 0.4968 0.7197
NW_003726273.1 67496 33588 0.4976 0.6784
NW_003726274.1 66523 33586 0.5049 0.721
NW_003726275.1 67057 33595 0.501 0.765
NW_003726276.1 66195 30600 0.4623 0.708
NW_003726277.1 87584 43484 0.4965 0.803
NW_003726278.1 84679 43495 0.5136 0.7504
NW_003726279.1 65840 32695 0.4966 0.689
NW_003726280.1 65696 33300 0.5069 0.7244
NW_003726281.1 66021 33000 0.4998 0.7783
NW_003726282.1 67300 30595 0.4546 0.7109
NW_003726283.1 88153 39900 0.4526 0.7408
NW_003726284.1 92437 43941 0.4754 0.7448
NW_003726285.1 70351 35082 0.4987 0.7501
NW_003726286.1 64646 35700 0.5522 0.7867
NW_003726287.1 69126 34200 0.4947 0.6878
NW_003726288.1 227674 101680 0.4466 0.9931
NW_003726289.1 64123 31496 0.4912 0.6999
NW_003726290.1 61944 30900 0.4988 0.693
NW_003726291.1 62414 32997 0.5287 0.6972
NW_003726292.1 61779 30899 0.5002 0.7234
NW_003726293.1 90840 42300 0.4657 0.7772
NW_003726294.1 61194 28500 0.4657 0.6887
NW_003726295.1 63245 26400 0.4174 0.6642
NW_003726296.1 60975 28800 0.4723 0.6718
NW_003726297.1 88336 41388 0.4685 0.7264
NW_003726298.1 62896 27000 0.4293 0.6731
NW_003726299.1 60346 30296 0.502 0.6593
NW_003726300.1 70666 32400 0.4585 0.752
NW_003726301.1 71007 40500 0.5704 0.7933
NW_003726302.1 59879 29096 0.4859 0.6977
NW_003726303.1 59817 32399 0.5416 0.7754
NW_003726304.1 66981 33300 0.4972 0.7664
NW_003726305.1 62805 31500 0.5016 0.727
NW_003726306.1 68857 34500 0.501 0.7403
NW_003726307.1 58149 33293 0.5725 0.7898
NW_003726308.1 84024 39595 0.4712 0.7821
NW_003726309.1 58658 28036 0.478 0.6817
NW_003726310.1 65402 33580 0.5134 0.7833
NW_003726311.1 56534 25800 0.4564 0.6651
NW_003726312.1 59023 30000 0.5083 0.6951
NW_003726313.1 89903 34500 0.3837 0.6907
NW_003726314.1 54477 32388 0.5945 0.7634
NW_003726315.1 54307 25800 0.4751 0.7132
NW_003726316.1 69310 31796 0.4588 0.7127
NW_003726317.1 57210 29700 0.5191 0.7976
NW_003726318.1 57907 28195 0.4869 0.7258
NW_003726319.1 53093 26697 0.5028 0.7018
NW_003726320.1 67358 28197 0.4186 0.6973
NW_003726321.1 54660 26995 0.4939 0.7158
NW_003726322.1 52548 27300 0.5195 0.7086
NW_003726323.1 52637 26396 0.5015 0.7229
NW_003726324.1 51964 25800 0.4965 0.6765
NW_003726325.1 51648 24600 0.4763 0.6419
NW_003726326.1 51582 24900 0.4827 0.6873
NW_003726327.1 52288 29097 0.5565 0.7654
NW_003726328.1 50462 25800 0.5113 0.7055
NW_003726329.1 50869 24900 0.4895 0.7241
NW_003726330.1 53506 27597 0.5158 0.7518
NW_003726331.1 50005 24596 0.4919 0.7336
NW_003726332.1 84691 31500 0.3719 0.6495
NW_003726333.1 63256 31200 0.4932 0.7196
NW_003726334.1 59752 27600 0.4619 0.7231
NW_003726335.1 68739 31800 0.4626 0.7948
NW_003726336.1 49027 26694 0.5445 0.803
NW_003726337.1 49032 23700 0.4834 0.6743
NW_003726338.1 57792 26542 0.4593 0.7237
NW_003726339.1 74646 33900 0.4541 0.8013
NW_003726340.1 48411 24600 0.5081 0.7533
NW_003726341.1 48200 22200 0.4606 0.6835
NW_003726342.1 75626 34491 0.4561 0.799
NW_003726343.1 48436 25200 0.5203 0.726
NW_003726344.1 47485 25200 0.5307 0.7764
NW_003726345.1 52731 24900 0.4722 0.6814
NW_003726346.1 52367 27000 0.5156 0.7296
NW_003726347.1 46689 22800 0.4883 0.6937
NW_003726348.1 53681 26097 0.4861 0.7287
NW_003726349.1 73441 32395 0.4411 0.7494
NW_003726350.1 57620 31193 0.5414 0.7867
NW_003726351.1 70154 32400 0.4618 0.8384
NW_003726352.1 67100 27594 0.4112 0.7263
NW_003726353.1 48085 24300 0.5054 0.7412
NW_003726354.1 63970 33300 0.5206 0.8105
NW_003726355.1 45242 21900 0.4841 0.6553
NW_003726356.1 58859 25195 0.4281 0.6859
NW_003726357.1 45065 19490 0.4325 0.6664
NW_003726358.1 46098 24900 0.5402 0.7011
NW_003726359.1 70370 31494 0.4475 0.7534
NW_003726360.1 46044 23996 0.5212 0.7607
NW_003726361.1 45518 22193 0.4876 0.6873
NW_003726362.1 47960 22200 0.4629 0.7561
NW_003726363.1 44571 22195 0.498 0.7328
NW_003726364.1 84617 38400 0.4538 0.8262
NW_003726365.1 51679 27900 0.5399 0.8366
NW_003726366.1 48264 25500 0.5283 0.771
NW_003726367.1 50939 22197 0.4358 0.6769
NW_003726368.1 72756 27900 0.3835 0.7369
NW_003726369.1 44216 17100 0.3867 0.6395
NW_003726370.1 43704 21900 0.5011 0.7197
NW_003726371.1 55991 27900 0.4983 0.7646
NW_003726372.1 54329 24600 0.4528 0.7287
NW_003726373.1 44549 23400 0.5253 0.7164
NW_003726374.1 44306 23086 0.5211 0.7046
NW_003726375.1 60428 24300 0.4021 0.7196
NW_003726376.1 42803 20700 0.4836 0.7221
NW_003726377.1 90666 41991 0.4631 0.8539
NW_003726378.1 42461 21000 0.4946 0.706
NW_003726379.1 46059 24000 0.5211 0.739
NW_003726380.1 58391 27296 0.4675 0.7343
NW_003726381.1 69503 30000 0.4316 0.7706
NW_003726382.1 41842 21900 0.5234 0.7361
NW_003726383.1 43189 23999 0.5557 0.7773
NW_003726384.1 42168 19800 0.4696 0.6742
NW_003726385.1 41454 21000 0.5066 0.6833
NW_003726386.1 43681 22200 0.5082 0.7388
NW_003726387.1 57311 30598 0.5339 0.8216
NW_003726388.1 68304 29100 0.426 0.727
NW_003726389.1 57240 26400 0.4612 0.7423
NW_003726390.1 42861 21900 0.511 0.8008
NW_003726391.1 43424 19200 0.4422 0.7087
NW_003726392.1 40931 19500 0.4764 0.7396
NW_003726393.1 41221 20100 0.4876 0.679
NW_003726394.1 41006 19197 0.4682 0.702
NW_003726395.1 40763 22050 0.5409 0.7341
NW_003726396.1 46509 21600 0.4644 0.7046
NW_003726397.1 42743 20400 0.4773 0.7498
NW_003726398.1 40517 19800 0.4887 0.6839
NW_003726399.1 40818 21293 0.5217 0.7275
NW_003726400.1 45697 27732 0.6069 0.8168
NW_003726401.1 46980 26100 0.5556 0.7605
NW_003726402.1 42806 20246 0.473 0.7251
NW_003726403.1 44573 25504 0.5722 0.78
NW_003726404.1 39716 19196 0.4833 0.6743
NW_003726405.1 39345 20100 0.5109 0.734
NW_003726406.1 46145 22200 0.4811 0.7273
NW_003726407.1 47441 24900 0.5249 0.7871
NW_003726408.1 39138 18600 0.4752 0.6923
NW_003726409.1 40677 20100 0.4941 0.7283
NW_003726410.1 64983 30595 0.4708 0.7953
NW_003726411.1 51094 26100 0.5108 0.7549
NW_003726412.1 38580 20100 0.521 0.7262
NW_003726413.1 40054 18895 0.4717 0.7073
NW_003726414.1 39199 19200 0.4898 0.7196
NW_003726415.1 38084 21600 0.5672 0.7717
NW_003726416.1 41432 20700 0.4996 0.7602
NW_003726417.1 45027 23095 0.5129 0.7342
NW_003726418.1 37707 21000 0.5569 0.7844
NW_003726419.1 59547 26986 0.4532 0.7635
NW_003726420.1 58434 27889 0.4773 0.8076
NW_003726421.1 37389 19196 0.5134 0.6535
NW_003726422.1 52308 25800 0.4932 0.8177
NW_003726423.1 63560 28497 0.4483 0.8158
NW_003726424.1 69036 31794 0.4605 0.8177
NW_003726425.1 44261 20395 0.4608 0.7268
NW_003726426.1 50023 25195 0.5037 0.8102
NW_003726427.1 36777 19498 0.5302 0.7583
NW_003726428.1 63789 31630 0.4959 0.8465
NW_003726429.1 56472 27292 0.4833 0.8495
NW_003726430.1 36805 19200 0.5217 0.6718
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NW_003729179.1 4577 3300 0.721 0.8758
NW_003729180.1 4577 2398 0.5239 0.7079
NW_003729181.1 4575 2400 0.5246 0.652
NW_003729182.1 4574 2100 0.4591 0.6572
NW_003729183.1 4572 2400 0.5249 0.7851
NW_003729184.1 4572 2100 0.4593 0.8441
NW_003729185.1 4562 2100 0.4603 0.6774
NW_003729186.1 4555 3300 0.7245 0.9976
NW_003729187.1 4554 3000 0.6588 0.7616
NW_003729188.1 4552 2100 0.4613 0.6524
NW_003729189.1 4550 2400 0.5275 0.651
NW_003729190.1 4543 3000 0.6604 0.749
NW_003729191.1 4541 2700 0.5946 0.6792
NW_003729192.1 4539 3300 0.727 0.839
NW_003729193.1 4527 2400 0.5302 0.7502
NW_003729194.1 4519 1800 0.3983 0.5798
NW_003729195.1 4507 3300 0.7322 0.7364
NW_003729196.1 4501 1500 0.3333 0.53
NW_003729197.1 4485 2400 0.5351 0.7478
NW_003729198.1 4480 2100 0.4688 0.5964
NW_003729199.1 4476 2100 0.4692 0.7528
NW_003729200.1 4469 2400 0.537 0.7505
NW_003729201.1 4463 1501 0.3363 0.5054
NW_003729202.1 4460 2100 0.4709 0.5863
NW_003729203.1 4454 2400 0.5388 0.6515
NW_003729204.1 4453 2100 0.4716 0.6225
NW_003729205.1 4447 1798 0.4043 0.5342
NW_003729206.1 4443 1800 0.4051 0.5072
NW_003729207.1 4439 2100 0.4731 0.586
NW_003729208.1 4437 2400 0.5409 0.7684
NW_003729209.1 4430 2400 0.5418 0.7572
NW_003729210.1 4429 1200 0.2709 0.5763
NW_003729211.1 4428 1800 0.4065 0.6596
NW_003729212.1 4420 2397 0.5423 0.8196
NW_003729213.1 4418 2100 0.4753 0.6014
NW_003729214.1 4418 1949 0.4411 0.611
NW_003729215.1 4408 1800 0.4083 0.6223
NW_003729216.1 4404 1800 0.4087 0.6968
NW_003729217.1 4404 2100 0.4768 0.6092
NW_003729218.1 4403 2100 0.4769 0.6465
NW_003729219.1 4399 2100 0.4774 0.7952
NW_003729220.1 4393 1495 0.3403 0.5642
NW_003729221.1 4389 3000 0.6835 0.6739
NW_003729222.1 4389 3900 0.8886 1.0848
NW_003729223.1 4388 2400 0.5469 0.6887
NW_003729224.1 4378 2400 0.5482 0.6626
NW_003729225.1 4368 1800 0.4121 0.5439
NW_003729226.1 4359 1800 0.4129 0.8448
NW_003729227.1 4356 2100 0.4821 0.5226
NW_003729228.1 4353 2400 0.5513 0.7727
NW_003729229.1 4329 2100 0.4851 0.8567
NW_003729230.1 4311 1800 0.4175 0.7264
NW_003729231.1 4302 2100 0.4881 0.7153
NW_003729232.1 4300 1798 0.4181 0.6427
NW_003729233.1 4285 1297 0.3027 0.5618
NW_003729234.1 4283 2696 0.6295 0.8835
NW_003729235.1 4282 2700 0.6305 0.6252
NW_003729236.1 4281 2700 0.6307 0.6741
NW_003729237.1 4279 2400 0.5609 0.7322
NW_003729238.1 4277 2400 0.5611 0.6515
NW_003729239.1 4276 2099 0.4909 0.5959
NW_003729240.1 4276 2400 0.5613 0.7129
NW_003729241.1 4252 2400 0.5644 0.6781
NW_003729242.1 4248 1800 0.4237 0.6004
NW_003729243.1 4239 1800 0.4246 0.6174
NW_003729244.1 4238 2696 0.6361 0.844
NW_003729245.1 4234 2400 0.5668 0.7172
NW_003729246.1 4233 1200 0.2835 0.5055
NW_003729247.1 4231 2700 0.6381 0.828
NW_003729248.1 4225 1200 0.284 0.5941
NW_003729249.1 4201 2700 0.6427 0.8272
NW_003729250.1 4198 2100 0.5002 0.7011
NW_003729251.1 4193 2099 0.5006 0.7104
NW_003729252.1 4186 1798 0.4295 0.5358
NW_003729253.1 4183 1200 0.2869 0.5444
NW_003729254.1 4177 1200 0.2873 0.5116
NW_003729255.1 4172 1797 0.4307 0.8097
NW_003729256.1 4163 2400 0.5765 0.7237
NW_003729257.1 4156 2700 0.6497 0.7558
NW_003729258.1 4141 2100 0.5071 0.8536
NW_003729259.1 4130 2100 0.5085 0.7563
NW_003729260.1 4130 1200 0.2906 0.5201
NW_003729261.1 4126 2996 0.7261 0.8641
NW_003729262.1 4123 2100 0.5093 0.6641
NW_003729263.1 4121 2400 0.5824 0.6816
NW_003729264.1 4117 1800 0.4372 0.7518
NW_003729265.1 4112 2100 0.5107 0.6252
NW_003729266.1 4097 2400 0.5858 0.6577
NW_003729267.1 4096 2695 0.658 0.7348
NW_003729268.1 4070 1795 0.441 0.5451
NW_003729269.1 4064 2090 0.5143 0.7406
NW_003729270.1 4061 2400 0.591 0.5975
NW_003729271.1 4060 1500 0.3695 0.6673
NW_003729272.1 4025 3000 0.7453 0.8561
NW_003729273.1 4025 2396 0.5953 0.672
NW_003729274.1 4011 2700 0.6731 0.6655
NW_003729275.1 4001 2100 0.5249 0.6537
NW_003729276.1 3976 2400 0.6036 0.9178
NW_003729277.1 3948 2100 0.5319 0.8259
NW_003729278.1 3941 2100 0.5329 0.6273
NW_003729279.1 3928 2550 0.6492 0.8605
NW_003729280.1 3925 900 0.2293 0.4204
NW_003729281.1 3919 2097 0.5351 0.8286
NW_003729282.1 3849 1200 0.3118 0.6378
NW_003729283.1 3848 900 0.2339 0.4233
NW_003729284.1 3847 2097 0.5451 0.7228
NW_003729285.1 3817 2100 0.5502 0.7203
NW_003729286.1 3780 1800 0.4762 0.6837
NW_003729287.1 3780 1800 0.4762 0.5636
NW_003729288.1 3777 1800 0.4766 0.8116
NW_003729289.1 3761 2100 0.5584 0.6513
NW_003729290.1 3750 2695 0.7187 0.8623
NW_003729291.1 3733 2400 0.6429 0.8575
NW_003729292.1 3719 900 0.242 0.4283
NW_003729293.1 3718 1200 0.3228 0.5928
NW_003729294.1 3706 1500 0.4047 0.6448
NW_003729295.1 3700 1200 0.3243 0.5329
NW_003729296.1 3695 2400 0.6495 0.6284
NW_003729297.1 3652 1800 0.4929 0.6975
NW_003729298.1 3649 1800 0.4933 0.6854
NW_003729299.1 3629 2100 0.5787 0.7616
NW_003729300.1 3622 1800 0.497 0.6017
NW_003729301.1 3616 1500 0.4148 0.5147
NW_003729302.1 3614 1500 0.4151 0.7196
NW_003729303.1 3595 1200 0.3338 0.6544
NW_003729304.1 3589 1200 0.3344 0.5538
NW_003729305.1 3585 1795 0.5007 0.6983
NW_003729306.1 3580 1200 0.3352 0.639
NW_003729307.1 3576 1800 0.5034 0.826
NW_003729308.1 3564 1500 0.4209 0.7481
NW_003729309.1 3524 1200 0.3405 0.6418
NW_003729310.1 3506 1500 0.4278 0.6014
NW_003729311.1 3484 1800 0.5166 0.6544
NW_003729312.1 3480 1500 0.431 0.7903
NW_003729313.1 3479 1800 0.5174 0.6821
NW_003729314.1 3440 2100 0.6105 0.5975
NW_003729315.1 3431 1800 0.5246 0.6734
NW_003729316.1 3430 1800 0.5248 0.666
NW_003729317.1 3407 1796 0.5271 0.6695
NW_003729318.1 3398 2100 0.618 0.7771
NW_003729319.1 3393 2400 0.7073 0.9457
NW_003729320.1 3388 1800 0.5313 0.6532
NW_003729321.1 3369 1190 0.3532 0.4817
NW_003729322.1 3338 900 0.2696 0.535
NW_003729323.1 3331 1800 0.5404 0.6365
NW_003729324.1 3271 1800 0.5503 0.7421
NW_003729325.1 3257 1200 0.3684 0.4956
NW_003729326.1 3257 1500 0.4605 0.7636
NW_003729327.1 3231 1500 0.4643 0.5352
NW_003729328.1 3135 2100 0.6699 0.8968
NW_003729329.1 3134 1499 0.4783 0.5442
NW_003729330.1 3059 1500 0.4904 0.6207
NW_003729331.1 3011 900 0.2989 0.4852
NW_003729332.1 2997 1200 0.4004 0.5664
NW_003729333.1 2955 900 0.3046 0.4661
NW_003729334.1 2933 900 0.3069 0.5357
NW_003729335.1 2850 1200 0.4211 0.663
NW_003729336.1 2823 1500 0.5313 0.7568
NW_003729337.1 2809 600 0.2136 0.571
NW_003729338.1 2772 898 0.324 0.5254
NW_003729339.1 2729 1500 0.5497 0.7627
NW_003729340.1 2708 1200 0.4431 0.6269
NW_003729341.1 2700 1200 0.4444 0.6724
NW_003729342.1 2641 900 0.3408 0.5362
NW_003729343.1 2494 1200 0.4812 0.6607
NW_003729344.1 2361 1498 0.6345 0.6667
NW_003729345.1 2327 1200 0.5157 0.7303
NW_003729346.1 2250 2100 0.9333 0.7339
NW_003729347.1 2145 1200 0.5594 0.7703
NW_003729348.1 2046 600 0.2933 0.6214
NW_003729349.1 1999 900 0.4502 0.5844
NW_003729350.1 1819 900 0.4948 0.6303
NW_003729351.1 1790 900 0.5028 0.5282
NW_003729352.1 1685 900 0.5341 0.8902
NW_003729353.1 1573 600 0.3814 0.5951
NW_003729354.1 1115 600 0.5381 0.7559
NC_002008.4 16727 8397 0.502 0.6516

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Mapped Reads Clipping Profile 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Input data & parameters
  • Summary
  • Coverage across reference
  • Coverage Histogram
  • Coverage Histogram (0-50X)
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped Reads Nucleotide Content
  • Mapped Reads GC-content Distribution
  • Mapped Reads Clipping Profile
  • Homopolymer Indels
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2025/07/30 17:41:59
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