Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/0.5X_no_error_med_variance/alignment/0.5X_no_error_med_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_no_error_med_variance/0.5X_no_error_med_variance_R1.fa results/0.5X_no_error_med_variance/0.5X_no_error_med_variance_R2.fa
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: bwa (0.7.19-r1273)
Analysis date: Wed Jul 30 17:41:47 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/0.5X_no_error_med_variance/alignment/0.5X_no_error_med_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 2 / 0%
Read min/max/mean length 45 / 150 / 150
Duplicated reads (estimated) 13,711 / 0.17%
Duplication rate 0.17%
Clipped reads 37,180 / 0.46%

ACGT Content

Number/percentage of A's 353,131,739 / 29.32%
Number/percentage of C's 249,129,684 / 20.68%
Number/percentage of T's 353,149,982 / 29.32%
Number/percentage of G's 249,124,793 / 20.68%
Number/percentage of N's 2,172 / 0%
GC Percentage 41.36%

Coverage

Mean 0.4999
Standard Deviation 0.7185

Mapping Quality

Mean Mapping Quality 32.31

Insert size

Mean 349.98
Standard Deviation 49.98
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 0.7%
Mismatches 7,640,343
Insertions 564,331
Mapped reads with at least one insertion 6.8%
Deletions 568,243
Mapped reads with at least one deletion 6.84%
Homopolymer indels 28.67%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 61403554 0.5005 0.7178
NC_006584.3 85426708 42870218 0.5018 0.7188
NC_006585.3 91889043 45973856 0.5003 0.7172
NC_006586.3 88276631 44181601 0.5005 0.7168
NC_006587.3 88915250 44467551 0.5001 0.7183
NC_006588.3 77573801 38807588 0.5003 0.7193
NC_006589.3 80974532 40501023 0.5002 0.7174
NC_006590.3 74330416 37181199 0.5002 0.7176
NC_006591.3 61074082 30604256 0.5011 0.7189
NC_006592.3 69331447 34661349 0.4999 0.7183
NC_006593.3 74389097 37189255 0.4999 0.7169
NC_006594.3 72498081 36230145 0.4997 0.717
NC_006595.3 63241923 31622232 0.5 0.7177
NC_006596.3 60966679 30483751 0.5 0.7184
NC_006597.3 64190966 32082627 0.4998 0.7187
NC_006598.3 59632846 29859098 0.5007 0.7184
NC_006599.3 64289059 32165955 0.5003 0.7181
NC_006600.3 55844845 27923160 0.5 0.7188
NC_006601.3 53741614 26870418 0.5 0.716
NC_006602.3 58134056 29063868 0.4999 0.7186
NC_006603.3 50858623 25435529 0.5001 0.717
NC_006604.3 61439934 30709787 0.4998 0.7178
NC_006605.3 52294480 26135407 0.4998 0.7157
NC_006606.3 47698779 23852652 0.5001 0.717
NC_006607.3 51628933 25810141 0.4999 0.7187
NC_006608.3 38964690 19494462 0.5003 0.7175
NC_006609.3 45876710 22923228 0.4997 0.7175
NC_006610.3 41182112 20575923 0.4996 0.7174
NC_006611.3 41845238 20902892 0.4995 0.7165
NC_006612.3 40214260 20099598 0.4998 0.7177
NC_006613.3 39895921 19945963 0.4999 0.7162
NC_006614.3 38810281 19394095 0.4997 0.7178
NC_006615.3 31377067 15693651 0.5002 0.7169
NC_006616.3 42124431 21058806 0.4999 0.7183
NC_006617.3 26524999 13263538 0.5 0.7177
NC_006618.3 30810995 15406542 0.5 0.7177
NC_006619.3 30902991 15445686 0.4998 0.7177
NC_006620.3 23914537 11955086 0.4999 0.7165
NC_006621.3 123869142 61897695 0.4997 0.718
NW_003726127.1 2660953 1329948 0.4998 0.7201
NW_003726128.1 1881673 951207 0.5055 0.7403
NW_003726129.1 1415205 709177 0.5011 0.7403
NW_003726130.1 1067467 538431 0.5044 0.7466
NW_003726131.1 866315 438829 0.5065 0.7244
NW_003726132.1 881102 443899 0.5038 0.7299
NW_003726133.1 822601 406451 0.4941 0.711
NW_003726134.1 741967 367165 0.4949 0.72
NW_003726135.1 745551 368916 0.4948 0.7313
NW_003726136.1 602611 300315 0.4984 0.708
NW_003726137.1 573630 285579 0.4978 0.7144
NW_003726138.1 666183 332987 0.4998 0.7626
NW_003726139.1 557017 279855 0.5024 0.7158
NW_003726140.1 510604 262404 0.5139 0.7212
NW_003726141.1 497093 257687 0.5184 0.7336
NW_003726142.1 492630 250782 0.5091 0.7423
NW_003726143.1 577062 283459 0.4912 0.7395
NW_003726144.1 561270 277506 0.4944 0.752
NW_003726145.1 407330 204616 0.5023 0.72
NW_003726146.1 405216 203342 0.5018 0.7257
NW_003726147.1 508668 256167 0.5036 0.7637
NW_003726148.1 540093 269373 0.4988 0.7861
NW_003726149.1 448434 222278 0.4957 0.747
NW_003726150.1 377800 187760 0.497 0.7208
NW_003726151.1 384880 192889 0.5012 0.7348
NW_003726152.1 367143 181200 0.4935 0.7159
NW_003726153.1 399987 202780 0.507 0.7452
NW_003726154.1 376204 190149 0.5054 0.7377
NW_003726155.1 416178 207873 0.4995 0.7471
NW_003726156.1 365470 183861 0.5031 0.7471
NW_003726157.1 322752 159979 0.4957 0.7202
NW_003726158.1 320591 161702 0.5044 0.7468
NW_003726159.1 310270 155669 0.5017 0.7164
NW_003726160.1 433650 216489 0.4992 0.7909
NW_003726161.1 273228 135625 0.4964 0.7097
NW_003726162.1 281659 140365 0.4984 0.7339
NW_003726163.1 320442 161969 0.5055 0.736
NW_003726164.1 265648 133784 0.5036 0.7335
NW_003726165.1 241365 122409 0.5072 0.6957
NW_003726166.1 234529 116962 0.4987 0.7226
NW_003726167.1 252720 127176 0.5032 0.7552
NW_003726168.1 254975 127788 0.5012 0.7164
NW_003726169.1 226053 113959 0.5041 0.7164
NW_003726170.1 223744 114626 0.5123 0.757
NW_003726171.1 227140 116677 0.5137 0.731
NW_003726172.1 219672 110983 0.5052 0.7445
NW_003726173.1 214597 110670 0.5157 0.7024
NW_003726174.1 386314 192236 0.4976 0.8363
NW_003726175.1 204342 100184 0.4903 0.734
NW_003726176.1 201724 101087 0.5011 0.7225
NW_003726177.1 216332 110374 0.5102 0.7464
NW_003726178.1 200877 100533 0.5005 0.7261
NW_003726179.1 310654 152090 0.4896 0.7922
NW_003726180.1 200932 100813 0.5017 0.6966
NW_003726181.1 201410 99259 0.4928 0.7094
NW_003726182.1 292533 142167 0.486 0.7946
NW_003726183.1 192561 95957 0.4983 0.6969
NW_003726184.1 210134 113095 0.5382 0.7734
NW_003726185.1 197844 100775 0.5094 0.7294
NW_003726186.1 196813 105309 0.5351 0.733
NW_003726187.1 180359 90588 0.5023 0.728
NW_003726188.1 210247 102306 0.4866 0.7217
NW_003726189.1 177735 89670 0.5045 0.7051
NW_003726190.1 172100 87001 0.5055 0.7137
NW_003726191.1 166866 83660 0.5014 0.7116
NW_003726192.1 164926 81584 0.4947 0.7418
NW_003726193.1 157598 79184 0.5024 0.7085
NW_003726194.1 143980 71981 0.4999 0.733
NW_003726195.1 141074 72016 0.5105 0.7234
NW_003726196.1 139526 69588 0.4987 0.7113
NW_003726197.1 142260 75572 0.5312 0.7384
NW_003726198.1 138160 69017 0.4995 0.7528
NW_003726199.1 142296 74079 0.5206 0.7593
NW_003726200.1 133119 67495 0.507 0.733
NW_003726201.1 129748 64476 0.4969 0.7278
NW_003726202.1 125962 67492 0.5358 0.7197
NW_003726203.1 127429 63891 0.5014 0.7326
NW_003726204.1 128261 64498 0.5029 0.7129
NW_003726205.1 131872 65708 0.4983 0.7493
NW_003726206.1 133432 70454 0.528 0.7825
NW_003726207.1 119670 57013 0.4764 0.6884
NW_003726208.1 144750 68673 0.4744 0.7543
NW_003726209.1 120779 59700 0.4943 0.7795
NW_003726210.1 115952 57601 0.4968 0.706
NW_003726211.1 118237 61488 0.52 0.7441
NW_003726212.1 111908 57303 0.5121 0.7147
NW_003726213.1 117332 59985 0.5112 0.8052
NW_003726214.1 111759 55804 0.4993 0.7305
NW_003726215.1 108801 57596 0.5294 0.7467
NW_003726216.1 112014 59681 0.5328 0.7267
NW_003726217.1 106428 56983 0.5354 0.7383
NW_003726218.1 104912 51279 0.4888 0.7074
NW_003726219.1 104646 52224 0.4991 0.7416
NW_003726220.1 103248 51881 0.5025 0.7034
NW_003726221.1 129482 62088 0.4795 0.7539
NW_003726222.1 118473 62690 0.5292 0.7705
NW_003726223.1 99993 48873 0.4888 0.6792
NW_003726224.1 109585 52798 0.4818 0.6843
NW_003726225.1 124049 62403 0.5031 0.7562
NW_003726226.1 99658 48600 0.4877 0.717
NW_003726227.1 101741 51905 0.5102 0.7223
NW_003726228.1 97365 48600 0.4992 0.7362
NW_003726229.1 94395 47675 0.5051 0.7175
NW_003726230.1 102992 57926 0.5624 0.8105
NW_003726231.1 95509 47384 0.4961 0.7329
NW_003726232.1 92047 45881 0.4985 0.7564
NW_003726233.1 87753 43174 0.492 0.7112
NW_003726234.1 96536 52477 0.5436 0.7772
NW_003726235.1 86544 45017 0.5202 0.7314
NW_003726236.1 85476 41694 0.4878 0.7475
NW_003726237.1 110512 57314 0.5186 0.7751
NW_003726238.1 83291 42278 0.5076 0.7059
NW_003726239.1 82459 43515 0.5277 0.7393
NW_003726240.1 81605 40195 0.4926 0.7134
NW_003726241.1 82380 42587 0.517 0.6978
NW_003726242.1 102198 48879 0.4783 0.7127
NW_003726243.1 82108 42017 0.5117 0.7417
NW_003726244.1 87041 41690 0.479 0.722
NW_003726245.1 79722 41700 0.5231 0.7393
NW_003726246.1 230124 110366 0.4796 0.9512
NW_003726247.1 78357 40201 0.513 0.6961
NW_003726248.1 256406 127535 0.4974 1.0615
NW_003726249.1 78050 40199 0.515 0.728
NW_003726250.1 81930 40499 0.4943 0.7431
NW_003726251.1 77100 39616 0.5138 0.7174
NW_003726252.1 77130 37480 0.4859 0.7122
NW_003726253.1 79078 40184 0.5082 0.6967
NW_003726254.1 90550 42589 0.4703 0.7234
NW_003726255.1 82767 39897 0.482 0.723
NW_003726256.1 89070 41399 0.4648 0.7201
NW_003726257.1 97802 48583 0.4967 0.7321
NW_003726258.1 79712 39884 0.5004 0.7262
NW_003726259.1 79581 42910 0.5392 0.7364
NW_003726260.1 73720 36605 0.4965 0.6904
NW_003726261.1 97799 47095 0.4815 0.7762
NW_003726262.1 73171 38089 0.5205 0.739
NW_003726263.1 104732 52812 0.5043 0.7892
NW_003726264.1 78935 38708 0.4904 0.7465
NW_003726265.1 72992 36591 0.5013 0.7028
NW_003726266.1 68721 34194 0.4976 0.7142
NW_003726267.1 73611 37186 0.5052 0.7443
NW_003726268.1 68272 33877 0.4962 0.7167
NW_003726269.1 79297 41099 0.5183 0.794
NW_003726270.1 84443 39587 0.4688 0.7305
NW_003726271.1 80679 37215 0.4613 0.784
NW_003726272.1 68834 33905 0.4926 0.7397
NW_003726273.1 67496 33587 0.4976 0.7332
NW_003726274.1 66523 36003 0.5412 0.757
NW_003726275.1 67057 33287 0.4964 0.736
NW_003726276.1 66195 33892 0.512 0.6923
NW_003726277.1 87584 45290 0.5171 0.8503
NW_003726278.1 84679 33298 0.3932 0.6844
NW_003726279.1 65840 32420 0.4924 0.7129
NW_003726280.1 65696 33614 0.5117 0.7167
NW_003726281.1 66021 33906 0.5136 0.7921
NW_003726282.1 67300 34489 0.5125 0.7074
NW_003726283.1 88153 41705 0.4731 0.7479
NW_003726284.1 92437 45115 0.4881 0.7861
NW_003726285.1 70351 33585 0.4774 0.7346
NW_003726286.1 64646 31491 0.4871 0.6972
NW_003726287.1 69126 32989 0.4772 0.76
NW_003726288.1 227674 103793 0.4559 1.0057
NW_003726289.1 64123 30008 0.468 0.6807
NW_003726290.1 61944 31199 0.5037 0.7204
NW_003726291.1 62414 32105 0.5144 0.7406
NW_003726292.1 61779 30904 0.5002 0.729
NW_003726293.1 90840 41106 0.4525 0.7745
NW_003726294.1 61194 30896 0.5049 0.7052
NW_003726295.1 63245 29685 0.4694 0.6811
NW_003726296.1 60975 31495 0.5165 0.7497
NW_003726297.1 88336 44706 0.5061 0.8083
NW_003726298.1 62896 29399 0.4674 0.678
NW_003726299.1 60346 32373 0.5365 0.7714
NW_003726300.1 70666 35994 0.5094 0.7703
NW_003726301.1 71007 34179 0.4813 0.7514
NW_003726302.1 59879 29703 0.4961 0.7052
NW_003726303.1 59817 32397 0.5416 0.7159
NW_003726304.1 66981 34212 0.5108 0.765
NW_003726305.1 62805 31789 0.5062 0.7558
NW_003726306.1 68857 34502 0.5011 0.7154
NW_003726307.1 58149 29406 0.5057 0.7394
NW_003726308.1 84024 40786 0.4854 0.8025
NW_003726309.1 58658 27900 0.4756 0.7029
NW_003726310.1 65402 33284 0.5089 0.7232
NW_003726311.1 56534 27292 0.4828 0.7307
NW_003726312.1 59023 28511 0.483 0.6997
NW_003726313.1 89903 40513 0.4506 0.7946
NW_003726314.1 54477 27904 0.5122 0.7239
NW_003726315.1 54307 31494 0.5799 0.8082
NW_003726316.1 69310 34178 0.4931 0.7637
NW_003726317.1 57210 28781 0.5031 0.7254
NW_003726318.1 57907 27013 0.4665 0.7349
NW_003726319.1 53093 26716 0.5032 0.7689
NW_003726320.1 67358 29396 0.4364 0.7705
NW_003726321.1 54660 27282 0.4991 0.7139
NW_003726322.1 52548 28476 0.5419 0.7706
NW_003726323.1 52637 27012 0.5132 0.6809
NW_003726324.1 51964 26114 0.5025 0.6789
NW_003726325.1 51648 28200 0.546 0.7466
NW_003726326.1 51582 28491 0.5523 0.7458
NW_003726327.1 52288 26991 0.5162 0.7695
NW_003726328.1 50462 26089 0.517 0.7532
NW_003726329.1 50869 27591 0.5424 0.7137
NW_003726330.1 53506 27903 0.5215 0.7736
NW_003726331.1 50005 24905 0.4981 0.7087
NW_003726332.1 84691 30596 0.3613 0.6625
NW_003726333.1 63256 30882 0.4882 0.7604
NW_003726334.1 59752 26686 0.4466 0.742
NW_003726335.1 68739 30599 0.4451 0.7453
NW_003726336.1 49027 23127 0.4717 0.7056
NW_003726337.1 49032 25193 0.5138 0.736
NW_003726338.1 57792 27579 0.4772 0.7126
NW_003726339.1 74646 34817 0.4664 0.7955
NW_003726340.1 48411 25490 0.5265 0.7955
NW_003726341.1 48200 23391 0.4853 0.7142
NW_003726342.1 75626 32993 0.4363 0.8401
NW_003726343.1 48436 24888 0.5138 0.7349
NW_003726344.1 47485 22493 0.4737 0.7237
NW_003726345.1 52731 24596 0.4664 0.7128
NW_003726346.1 52367 27288 0.5211 0.7697
NW_003726347.1 46689 22817 0.4887 0.7174
NW_003726348.1 53681 26403 0.4919 0.7202
NW_003726349.1 73441 28480 0.3878 0.6697
NW_003726350.1 57620 26415 0.4584 0.7646
NW_003726351.1 70154 31171 0.4443 0.7646
NW_003726352.1 67100 28489 0.4246 0.6961
NW_003726353.1 48085 23689 0.4926 0.7176
NW_003726354.1 63970 30299 0.4736 0.7537
NW_003726355.1 45242 22190 0.4905 0.7241
NW_003726356.1 58859 26981 0.4584 0.7226
NW_003726357.1 45065 19794 0.4392 0.6711
NW_003726358.1 46098 23401 0.5076 0.7605
NW_003726359.1 70370 29085 0.4133 0.7095
NW_003726360.1 46044 20694 0.4494 0.7182
NW_003726361.1 45518 26094 0.5733 0.7732
NW_003726362.1 47960 24000 0.5004 0.7205
NW_003726363.1 44571 21902 0.4914 0.7051
NW_003726364.1 84617 35400 0.4184 0.7696
NW_003726365.1 51679 27572 0.5335 0.7837
NW_003726366.1 48264 24598 0.5097 0.7851
NW_003726367.1 50939 25202 0.4947 0.7597
NW_003726368.1 72756 32705 0.4495 0.7765
NW_003726369.1 44216 25212 0.5702 0.6881
NW_003726370.1 43704 21901 0.5011 0.7083
NW_003726371.1 55991 24012 0.4289 0.7066
NW_003726372.1 54329 22210 0.4088 0.6878
NW_003726373.1 44549 20983 0.471 0.6946
NW_003726374.1 44306 22175 0.5005 0.7146
NW_003726375.1 60428 24301 0.4021 0.7447
NW_003726376.1 42803 20997 0.4905 0.7331
NW_003726377.1 90666 44401 0.4897 0.8732
NW_003726378.1 42461 22189 0.5226 0.7414
NW_003726379.1 46059 23107 0.5017 0.7849
NW_003726380.1 58391 27281 0.4672 0.7867
NW_003726381.1 69503 29693 0.4272 0.7601
NW_003726382.1 41842 20694 0.4946 0.7333
NW_003726383.1 43189 22793 0.5278 0.7514
NW_003726384.1 42168 24016 0.5695 0.7833
NW_003726385.1 41454 21612 0.5213 0.7096
NW_003726386.1 43681 22521 0.5156 0.7423
NW_003726387.1 57311 27600 0.4816 0.7592
NW_003726388.1 68304 30603 0.448 0.7556
NW_003726389.1 57240 26400 0.4612 0.7545
NW_003726390.1 42861 20405 0.4761 0.7348
NW_003726391.1 43424 23410 0.5391 0.6838
NW_003726392.1 40931 20405 0.4985 0.7329
NW_003726393.1 41221 21613 0.5243 0.7346
NW_003726394.1 41006 19780 0.4824 0.6838
NW_003726395.1 40763 20102 0.4931 0.664
NW_003726396.1 46509 23990 0.5158 0.6805
NW_003726397.1 42743 20095 0.4701 0.6795
NW_003726398.1 40517 21596 0.533 0.7537
NW_003726399.1 40818 20699 0.5071 0.6652
NW_003726400.1 45697 21606 0.4728 0.7742
NW_003726401.1 46980 21286 0.4531 0.7189
NW_003726402.1 42806 23098 0.5396 0.7807
NW_003726403.1 44573 23684 0.5314 0.8155
NW_003726404.1 39716 19805 0.4987 0.6928
NW_003726405.1 39345 23399 0.5947 0.8179
NW_003726406.1 46145 23986 0.5198 0.77
NW_003726407.1 47441 24598 0.5185 0.754
NW_003726408.1 39138 20703 0.529 0.7078
NW_003726409.1 40677 20408 0.5017 0.7111
NW_003726410.1 64983 29395 0.4523 0.8062
NW_003726411.1 51094 23712 0.4641 0.7733
NW_003726412.1 38580 21016 0.5447 0.7147
NW_003726413.1 40054 20109 0.502 0.7377
NW_003726414.1 39199 17400 0.4439 0.7124
NW_003726415.1 38084 18599 0.4884 0.7042
NW_003726416.1 41432 20995 0.5067 0.7286
NW_003726417.1 45027 20095 0.4463 0.7059
NW_003726418.1 37707 18609 0.4935 0.7279
NW_003726419.1 59547 29404 0.4938 0.8119
NW_003726420.1 58434 26376 0.4514 0.7863
NW_003726421.1 37389 18599 0.4974 0.714
NW_003726422.1 52308 22194 0.4243 0.7216
NW_003726423.1 63560 30295 0.4766 0.8043
NW_003726424.1 69036 32698 0.4736 0.8466
NW_003726425.1 44261 22189 0.5013 0.7742
NW_003726426.1 50023 23699 0.4738 0.7905
NW_003726427.1 36777 17996 0.4893 0.7281
NW_003726428.1 63789 29085 0.456 0.7594
NW_003726429.1 56472 26387 0.4673 0.7649
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NW_003729171.1 4612 2102 0.4558 0.7722
NW_003729172.1 4601 2695 0.5857 0.7673
NW_003729173.1 4600 2401 0.522 0.6547
NW_003729174.1 4600 2700 0.587 0.7975
NW_003729175.1 4594 2101 0.4573 0.6888
NW_003729176.1 4588 1795 0.3912 0.5806
NW_003729177.1 4580 2700 0.5895 0.8758
NW_003729178.1 4577 2399 0.5241 0.6398
NW_003729179.1 4577 2994 0.6541 0.6786
NW_003729180.1 4577 2400 0.5244 0.6639
NW_003729181.1 4575 2700 0.5902 0.7531
NW_003729182.1 4574 3000 0.6559 0.7426
NW_003729183.1 4572 2099 0.4591 0.6866
NW_003729184.1 4572 2100 0.4593 0.7635
NW_003729185.1 4562 2698 0.5914 0.6441
NW_003729186.1 4555 2402 0.5273 0.6358
NW_003729187.1 4554 3298 0.7242 0.7573
NW_003729188.1 4552 3601 0.7911 0.8968
NW_003729189.1 4550 2700 0.5934 0.8283
NW_003729190.1 4543 2702 0.5948 0.7077
NW_003729191.1 4541 2099 0.4622 0.6269
NW_003729192.1 4539 3602 0.7936 0.7413
NW_003729193.1 4527 3301 0.7292 0.8123
NW_003729194.1 4519 3298 0.7298 1.0514
NW_003729195.1 4507 2101 0.4662 0.6714
NW_003729196.1 4501 2699 0.5996 0.8209
NW_003729197.1 4485 2402 0.5356 0.8611
NW_003729198.1 4480 1500 0.3348 0.5088
NW_003729199.1 4476 2100 0.4692 0.6561
NW_003729200.1 4469 2108 0.4717 0.7843
NW_003729201.1 4463 2100 0.4705 0.8286
NW_003729202.1 4460 1500 0.3363 0.4729
NW_003729203.1 4454 2402 0.5393 0.7284
NW_003729204.1 4453 2099 0.4714 0.6079
NW_003729205.1 4447 2402 0.5401 0.6838
NW_003729206.1 4443 1799 0.4049 0.528
NW_003729207.1 4439 2101 0.4733 0.6298
NW_003729208.1 4437 2100 0.4733 0.7391
NW_003729209.1 4430 1804 0.4072 0.6156
NW_003729210.1 4429 3000 0.6774 0.8337
NW_003729211.1 4428 1800 0.4065 0.6741
NW_003729212.1 4420 3292 0.7448 0.772
NW_003729213.1 4418 2689 0.6086 0.7841
NW_003729214.1 4418 2101 0.4756 0.7788
NW_003729215.1 4408 1802 0.4088 0.5185
NW_003729216.1 4404 2398 0.5445 0.6981
NW_003729217.1 4404 1499 0.3404 0.6192
NW_003729218.1 4403 2100 0.4769 0.6312
NW_003729219.1 4399 1802 0.4096 0.7132
NW_003729220.1 4393 3303 0.7519 0.8257
NW_003729221.1 4389 1800 0.4101 0.7111
NW_003729222.1 4389 3600 0.8202 0.7744
NW_003729223.1 4388 2099 0.4784 0.6637
NW_003729224.1 4378 1201 0.2743 0.4461
NW_003729225.1 4368 2400 0.5495 0.8295
NW_003729226.1 4359 1500 0.3441 0.4756
NW_003729227.1 4356 2102 0.4826 0.6007
NW_003729228.1 4353 2097 0.4817 0.5781
NW_003729229.1 4329 2099 0.4849 0.9505
NW_003729230.1 4311 2400 0.5567 0.7745
NW_003729231.1 4302 1498 0.3482 0.5862
NW_003729232.1 4300 1800 0.4186 0.6146
NW_003729233.1 4285 2100 0.4901 0.6979
NW_003729234.1 4283 2388 0.5576 0.7897
NW_003729235.1 4282 1202 0.2807 0.4778
NW_003729236.1 4281 2698 0.6302 0.699
NW_003729237.1 4279 2100 0.4908 0.7318
NW_003729238.1 4277 2101 0.4912 0.6709
NW_003729239.1 4276 1804 0.4219 0.5803
NW_003729240.1 4276 2997 0.7009 0.7403
NW_003729241.1 4252 2101 0.4941 0.6291
NW_003729242.1 4248 2104 0.4953 0.5781
NW_003729243.1 4239 2700 0.6369 1.0678
NW_003729244.1 4238 901 0.2126 0.4798
NW_003729245.1 4234 1496 0.3533 0.5484
NW_003729246.1 4233 2103 0.4968 0.7226
NW_003729247.1 4231 2103 0.497 0.6802
NW_003729248.1 4225 1795 0.4249 0.8505
NW_003729249.1 4201 2100 0.4999 0.6855
NW_003729250.1 4198 1502 0.3578 0.49
NW_003729251.1 4193 1500 0.3577 0.6801
NW_003729252.1 4186 3001 0.7169 1.0215
NW_003729253.1 4183 2394 0.5723 0.6956
NW_003729254.1 4177 1502 0.3596 0.5255
NW_003729255.1 4172 1199 0.2874 0.6091
NW_003729256.1 4163 2402 0.577 0.6376
NW_003729257.1 4156 1187 0.2856 0.8471
NW_003729258.1 4141 1800 0.4347 0.697
NW_003729259.1 4130 2098 0.508 0.6733
NW_003729260.1 4130 2096 0.5075 0.7608
NW_003729261.1 4126 1493 0.3619 0.8505
NW_003729262.1 4123 2404 0.5831 0.9839
NW_003729263.1 4121 2401 0.5826 0.7901
NW_003729264.1 4117 1800 0.4372 0.6018
NW_003729265.1 4112 1803 0.4385 0.7328
NW_003729266.1 4097 1797 0.4386 0.6469
NW_003729267.1 4096 2698 0.6587 0.73
NW_003729268.1 4070 2100 0.516 0.608
NW_003729269.1 4064 2698 0.6639 0.8449
NW_003729270.1 4061 1500 0.3694 0.8232
NW_003729271.1 4060 2698 0.6645 0.7252
NW_003729272.1 4025 2402 0.5968 0.8011
NW_003729273.1 4025 2100 0.5217 0.7658
NW_003729274.1 4011 2402 0.5989 0.6952
NW_003729275.1 4001 1800 0.4499 0.702
NW_003729276.1 3976 1206 0.3033 0.6026
NW_003729277.1 3948 2100 0.5319 0.7743
NW_003729278.1 3941 2702 0.6856 0.7794
NW_003729279.1 3928 1501 0.3821 0.58
NW_003729280.1 3925 1495 0.3809 0.6388
NW_003729281.1 3919 1799 0.459 0.4983
NW_003729282.1 3849 2099 0.5453 0.6118
NW_003729283.1 3848 1502 0.3903 0.7153
NW_003729284.1 3847 2101 0.5461 0.6863
NW_003729285.1 3817 2402 0.6293 0.696
NW_003729286.1 3780 1796 0.4751 0.7483
NW_003729287.1 3780 900 0.2381 0.4524
NW_003729288.1 3777 1799 0.4763 0.6285
NW_003729289.1 3761 1495 0.3975 0.564
NW_003729290.1 3750 3301 0.8803 0.9868
NW_003729291.1 3733 2101 0.5628 0.6666
NW_003729292.1 3719 1800 0.484 0.6272
NW_003729293.1 3718 2396 0.6444 0.8011
NW_003729294.1 3706 1799 0.4854 0.7279
NW_003729295.1 3700 2395 0.6473 0.7973
NW_003729296.1 3695 1496 0.4049 0.705
NW_003729297.1 3652 1798 0.4923 0.6268
NW_003729298.1 3649 1501 0.4113 0.7458
NW_003729299.1 3629 1800 0.496 0.7329
NW_003729300.1 3622 1803 0.4978 0.7001
NW_003729301.1 3616 1802 0.4983 0.6726
NW_003729302.1 3614 2098 0.5805 0.667
NW_003729303.1 3595 2389 0.6645 0.748
NW_003729304.1 3589 2104 0.5862 0.6981
NW_003729305.1 3585 1801 0.5024 0.5689
NW_003729306.1 3580 1501 0.4193 0.4957
NW_003729307.1 3576 2096 0.5861 0.8653
NW_003729308.1 3564 1794 0.5034 0.6037
NW_003729309.1 3524 1800 0.5108 0.7076
NW_003729310.1 3506 1201 0.3426 0.6031
NW_003729311.1 3484 1500 0.4305 0.7108
NW_003729312.1 3480 1201 0.3451 0.5131
NW_003729313.1 3479 1499 0.4309 0.5078
NW_003729314.1 3440 1500 0.436 0.5075
NW_003729315.1 3431 2104 0.6132 0.694
NW_003729316.1 3430 1799 0.5245 0.715
NW_003729317.1 3407 1798 0.5277 0.6898
NW_003729318.1 3398 2090 0.6151 0.8638
NW_003729319.1 3393 1201 0.354 0.5572
NW_003729320.1 3388 1801 0.5316 0.717
NW_003729321.1 3369 595 0.1766 0.3971
NW_003729322.1 3338 2105 0.6306 0.7341
NW_003729323.1 3331 1202 0.3609 0.5581
NW_003729324.1 3271 1804 0.5515 0.5907
NW_003729325.1 3257 1200 0.3684 0.544
NW_003729326.1 3257 1501 0.4609 0.6455
NW_003729327.1 3231 1801 0.5574 0.8118
NW_003729328.1 3135 1799 0.5738 0.8115
NW_003729329.1 3134 2100 0.6701 0.8144
NW_003729330.1 3059 1503 0.4913 0.9305
NW_003729331.1 3011 1801 0.5981 0.7964
NW_003729332.1 2997 1198 0.3997 0.6116
NW_003729333.1 2955 1500 0.5076 0.6725
NW_003729334.1 2933 900 0.3069 0.5287
NW_003729335.1 2850 901 0.3161 0.4648
NW_003729336.1 2823 1800 0.6376 0.9501
NW_003729337.1 2809 1800 0.6408 0.7435
NW_003729338.1 2772 600 0.2165 0.525
NW_003729339.1 2729 1502 0.5504 0.7988
NW_003729340.1 2708 1500 0.5539 0.8497
NW_003729341.1 2700 600 0.2222 0.4157
NW_003729342.1 2641 898 0.34 0.5374
NW_003729343.1 2494 1188 0.4763 0.8377
NW_003729344.1 2361 1793 0.7594 0.6235
NW_003729345.1 2327 1199 0.5153 0.7238
NW_003729346.1 2250 1198 0.5324 0.6587
NW_003729347.1 2145 1199 0.559 0.611
NW_003729348.1 2046 600 0.2933 0.5671
NW_003729349.1 1999 1500 0.7504 0.6946
NW_003729350.1 1819 901 0.4953 0.7107
NW_003729351.1 1790 300 0.1676 0.3735
NW_003729352.1 1685 900 0.5341 0.571
NW_003729353.1 1573 1194 0.7591 0.9958
NW_003729354.1 1115 299 0.2682 0.443
NC_002008.4 16727 8400 0.5022 0.6799

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 17:41:48
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