Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/0.5X_hi_error_low_variance/alignment/0.5X_hi_error_low_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_hi_error_low_variance/0.5X_hi_error_low_variance_R1.fa results/0.5X_hi_error_low_variance/0.5X_hi_error_low_variance_R2.fa
Draw chromosome limits: no
Analyze overlapping paired-end reads: no
Program: bwa (0.7.19-r1273)
Analysis date: Wed Jul 30 17:33:05 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/0.5X_hi_error_low_variance/alignment/0.5X_hi_error_low_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 8,036,542
Mapped reads 8,036,515 / 100%
Unmapped reads 27 / 0%
Mapped paired reads 8,036,515 / 100%
Mapped reads, first in pair 4,018,258 / 50%
Mapped reads, second in pair 4,018,257 / 50%
Mapped reads, both in pair 8,036,494 / 100%
Mapped reads, singletons 21 / 0%
Secondary alignments 0
Supplementary alignments 162 / 0%
Read min/max/mean length 30 / 150 / 150
Duplicated reads (estimated) 13,651 / 0.17%
Duplication rate 0.17%
Clipped reads 535,425 / 6.66%

ACGT Content

Number/percentage of A's 352,663,004 / 29.35%
Number/percentage of C's 253,210,263 / 21.08%
Number/percentage of T's 347,513,859 / 28.92%
Number/percentage of G's 248,054,343 / 20.65%
Number/percentage of N's 2,115 / 0%
GC Percentage 41.72%

Coverage

Mean 0.4984
Standard Deviation 0.7179

Mapping Quality

Mean Mapping Quality 30.78

Insert size

Mean 507.98
Standard Deviation 82,142.35
P25/Median/P75 316 / 350 / 383

Mismatches and indels

General error rate 4.96%
Mismatches 59,499,573
Insertions 62,395
Mapped reads with at least one insertion 0.77%
Deletions 61,114
Mapped reads with at least one deletion 0.76%
Homopolymer indels 27.62%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 61182671 0.4987 0.7167
NC_006584.3 85426708 42718818 0.5001 0.7191
NC_006585.3 91889043 45820418 0.4986 0.7175
NC_006586.3 88276631 44034939 0.4988 0.717
NC_006587.3 88915250 44336082 0.4986 0.7177
NC_006588.3 77573801 38683982 0.4987 0.7185
NC_006589.3 80974532 40372078 0.4986 0.7169
NC_006590.3 74330416 37104570 0.4992 0.7181
NC_006591.3 61074082 30484966 0.4991 0.7182
NC_006592.3 69331447 34560557 0.4985 0.7169
NC_006593.3 74389097 37081945 0.4985 0.7161
NC_006594.3 72498081 36126983 0.4983 0.7159
NC_006595.3 63241923 31529315 0.4986 0.7161
NC_006596.3 60966679 30401634 0.4987 0.7181
NC_006597.3 64190966 31987068 0.4983 0.7172
NC_006598.3 59632846 29761387 0.4991 0.7174
NC_006599.3 64289059 32033371 0.4983 0.7165
NC_006600.3 55844845 27826283 0.4983 0.717
NC_006601.3 53741614 26792769 0.4985 0.7154
NC_006602.3 58134056 28971005 0.4983 0.7159
NC_006603.3 50858623 25346732 0.4984 0.7183
NC_006604.3 61439934 30604624 0.4981 0.7167
NC_006605.3 52294480 26064379 0.4984 0.7163
NC_006606.3 47698779 23768884 0.4983 0.7162
NC_006607.3 51628933 25720226 0.4982 0.7147
NC_006608.3 38964690 19450542 0.4992 0.7184
NC_006609.3 45876710 22861974 0.4983 0.7162
NC_006610.3 41182112 20524333 0.4984 0.7183
NC_006611.3 41845238 20833778 0.4979 0.7161
NC_006612.3 40214260 20045243 0.4985 0.7156
NC_006613.3 39895921 19881879 0.4983 0.7176
NC_006614.3 38810281 19322794 0.4979 0.7163
NC_006615.3 31377067 15632698 0.4982 0.7155
NC_006616.3 42124431 20989947 0.4983 0.7186
NC_006617.3 26524999 13208413 0.498 0.7131
NC_006618.3 30810995 15354281 0.4983 0.7192
NC_006619.3 30902991 15405338 0.4985 0.7176
NC_006620.3 23914537 11924412 0.4986 0.7174
NC_006621.3 123869142 61707652 0.4982 0.7173
NW_003726127.1 2660953 1335827 0.502 0.7251
NW_003726128.1 1881673 930968 0.4948 0.7388
NW_003726129.1 1415205 705023 0.4982 0.7281
NW_003726130.1 1067467 533247 0.4995 0.7486
NW_003726131.1 866315 437133 0.5046 0.7308
NW_003726132.1 881102 440486 0.4999 0.7313
NW_003726133.1 822601 416956 0.5069 0.7472
NW_003726134.1 741967 370145 0.4989 0.7205
NW_003726135.1 745551 371872 0.4988 0.7503
NW_003726136.1 602611 306652 0.5089 0.7238
NW_003726137.1 573630 282986 0.4933 0.7055
NW_003726138.1 666183 333484 0.5006 0.7555
NW_003726139.1 557017 281969 0.5062 0.7386
NW_003726140.1 510604 251028 0.4916 0.7186
NW_003726141.1 497093 251424 0.5058 0.7266
NW_003726142.1 492630 249065 0.5056 0.7281
NW_003726143.1 577062 290518 0.5034 0.7764
NW_003726144.1 561270 279529 0.498 0.7566
NW_003726145.1 407330 201962 0.4958 0.7171
NW_003726146.1 405216 202715 0.5003 0.7078
NW_003726147.1 508668 259411 0.51 0.7811
NW_003726148.1 540093 273673 0.5067 0.8056
NW_003726149.1 448434 220686 0.4921 0.7502
NW_003726150.1 377800 193829 0.513 0.7324
NW_003726151.1 384880 195519 0.508 0.7367
NW_003726152.1 367143 185816 0.5061 0.7408
NW_003726153.1 399987 201147 0.5029 0.7277
NW_003726154.1 376204 189102 0.5027 0.7473
NW_003726155.1 416178 206581 0.4964 0.7453
NW_003726156.1 365470 184129 0.5038 0.7352
NW_003726157.1 322752 169691 0.5258 0.7453
NW_003726158.1 320591 159353 0.4971 0.7152
NW_003726159.1 310270 155720 0.5019 0.7303
NW_003726160.1 433650 209046 0.4821 0.7839
NW_003726161.1 273228 135194 0.4948 0.7073
NW_003726162.1 281659 138986 0.4935 0.7125
NW_003726163.1 320442 158828 0.4957 0.7454
NW_003726164.1 265648 130971 0.493 0.7158
NW_003726165.1 241365 125186 0.5187 0.7235
NW_003726166.1 234529 114495 0.4882 0.6998
NW_003726167.1 252720 123268 0.4878 0.7347
NW_003726168.1 254975 126319 0.4954 0.7216
NW_003726169.1 226053 112431 0.4974 0.7407
NW_003726170.1 223744 114845 0.5133 0.7318
NW_003726171.1 227140 115984 0.5106 0.7291
NW_003726172.1 219672 108793 0.4953 0.71
NW_003726173.1 214597 108222 0.5043 0.7066
NW_003726174.1 386314 192315 0.4978 0.8707
NW_003726175.1 204342 104317 0.5105 0.7134
NW_003726176.1 201724 100543 0.4984 0.7232
NW_003726177.1 216332 108813 0.503 0.7545
NW_003726178.1 200877 101468 0.5051 0.7353
NW_003726179.1 310654 151572 0.4879 0.8227
NW_003726180.1 200932 100502 0.5002 0.7476
NW_003726181.1 201410 99268 0.4929 0.7184
NW_003726182.1 292533 144191 0.4929 0.8076
NW_003726183.1 192561 95636 0.4967 0.7162
NW_003726184.1 210134 102493 0.4878 0.7296
NW_003726185.1 197844 102600 0.5186 0.7239
NW_003726186.1 196813 102548 0.521 0.7661
NW_003726187.1 180359 90007 0.499 0.701
NW_003726188.1 210247 100813 0.4795 0.7476
NW_003726189.1 177735 90055 0.5067 0.7428
NW_003726190.1 172100 90304 0.5247 0.7282
NW_003726191.1 166866 84929 0.509 0.7266
NW_003726192.1 164926 86455 0.5242 0.7508
NW_003726193.1 157598 75987 0.4822 0.7293
NW_003726194.1 143980 71752 0.4983 0.7103
NW_003726195.1 141074 69305 0.4913 0.7042
NW_003726196.1 139526 70859 0.5079 0.7475
NW_003726197.1 142260 69627 0.4894 0.7381
NW_003726198.1 138160 69933 0.5062 0.7086
NW_003726199.1 142296 69003 0.4849 0.7583
NW_003726200.1 133119 65102 0.4891 0.7348
NW_003726201.1 129748 64329 0.4958 0.707
NW_003726202.1 125962 66685 0.5294 0.7262
NW_003726203.1 127429 63066 0.4949 0.7154
NW_003726204.1 128261 65391 0.5098 0.7595
NW_003726205.1 131872 65418 0.4961 0.7001
NW_003726206.1 133432 62958 0.4718 0.7372
NW_003726207.1 119670 58623 0.4899 0.6677
NW_003726208.1 144750 67845 0.4687 0.6937
NW_003726209.1 120779 63064 0.5221 0.7479
NW_003726210.1 115952 60950 0.5256 0.7619
NW_003726211.1 118237 59176 0.5005 0.7438
NW_003726212.1 111908 53169 0.4751 0.7596
NW_003726213.1 117332 61323 0.5226 0.7244
NW_003726214.1 111759 55634 0.4978 0.6955
NW_003726215.1 108801 60332 0.5545 0.7544
NW_003726216.1 112014 56229 0.502 0.6987
NW_003726217.1 106428 52112 0.4896 0.6775
NW_003726218.1 104912 54700 0.5214 0.7694
NW_003726219.1 104646 49633 0.4743 0.7317
NW_003726220.1 103248 50078 0.485 0.6954
NW_003726221.1 129482 63787 0.4926 0.7462
NW_003726222.1 118473 59787 0.5046 0.8139
NW_003726223.1 99993 51134 0.5114 0.7223
NW_003726224.1 109585 53827 0.4912 0.7122
NW_003726225.1 124049 61287 0.4941 0.7746
NW_003726226.1 99658 48658 0.4882 0.7189
NW_003726227.1 101741 50563 0.497 0.6996
NW_003726228.1 97365 48623 0.4994 0.721
NW_003726229.1 94395 45811 0.4853 0.6558
NW_003726230.1 102992 51801 0.503 0.7428
NW_003726231.1 95509 47843 0.5009 0.7559
NW_003726232.1 92047 46034 0.5001 0.7033
NW_003726233.1 87753 44915 0.5118 0.6978
NW_003726234.1 96536 43098 0.4464 0.7378
NW_003726235.1 86544 42869 0.4953 0.6915
NW_003726236.1 85476 43044 0.5036 0.7251
NW_003726237.1 110512 57760 0.5227 0.791
NW_003726238.1 83291 41210 0.4948 0.7033
NW_003726239.1 82459 42378 0.5139 0.7009
NW_003726240.1 81605 43946 0.5385 0.7538
NW_003726241.1 82380 42420 0.5149 0.775
NW_003726242.1 102198 49090 0.4803 0.7234
NW_003726243.1 82108 42201 0.514 0.7128
NW_003726244.1 87041 43514 0.4999 0.726
NW_003726245.1 79722 39745 0.4985 0.6844
NW_003726246.1 230124 111239 0.4834 0.9825
NW_003726247.1 78357 39743 0.5072 0.7164
NW_003726248.1 256406 124032 0.4837 1.0251
NW_003726249.1 78050 39940 0.5117 0.7234
NW_003726250.1 81930 42617 0.5202 0.7207
NW_003726251.1 77100 38251 0.4961 0.7233
NW_003726252.1 77130 38951 0.505 0.6903
NW_003726253.1 79078 37677 0.4765 0.7271
NW_003726254.1 90550 46060 0.5087 0.7861
NW_003726255.1 82767 40088 0.4843 0.7151
NW_003726256.1 89070 44301 0.4974 0.7895
NW_003726257.1 97802 48657 0.4975 0.7328
NW_003726258.1 79712 39781 0.4991 0.7664
NW_003726259.1 79581 41454 0.5209 0.7727
NW_003726260.1 73720 37872 0.5137 0.7578
NW_003726261.1 97799 47572 0.4864 0.7632
NW_003726262.1 73171 36169 0.4943 0.688
NW_003726263.1 104732 51697 0.4936 0.8001
NW_003726264.1 78935 40363 0.5113 0.7366
NW_003726265.1 72992 38254 0.5241 0.7107
NW_003726266.1 68721 33189 0.483 0.7169
NW_003726267.1 73611 36514 0.496 0.7168
NW_003726268.1 68272 34139 0.5 0.7253
NW_003726269.1 79297 35864 0.4523 0.7285
NW_003726270.1 84443 39685 0.47 0.7146
NW_003726271.1 80679 35595 0.4412 0.7327
NW_003726272.1 68834 33448 0.4859 0.704
NW_003726273.1 67496 33509 0.4965 0.7002
NW_003726274.1 66523 34105 0.5127 0.7212
NW_003726275.1 67057 32891 0.4905 0.679
NW_003726276.1 66195 32823 0.4959 0.6741
NW_003726277.1 87584 40282 0.4599 0.7277
NW_003726278.1 84679 44205 0.522 0.7908
NW_003726279.1 65840 31441 0.4775 0.6575
NW_003726280.1 65696 32921 0.5011 0.7437
NW_003726281.1 66021 33748 0.5112 0.7265
NW_003726282.1 67300 35683 0.5302 0.7493
NW_003726283.1 88153 42072 0.4773 0.7758
NW_003726284.1 92437 47545 0.5144 0.8029
NW_003726285.1 70351 35321 0.5021 0.7666
NW_003726286.1 64646 31645 0.4895 0.7421
NW_003726287.1 69126 35424 0.5125 0.7671
NW_003726288.1 227674 99501 0.437 0.9726
NW_003726289.1 64123 33788 0.5269 0.7262
NW_003726290.1 61944 29870 0.4822 0.7052
NW_003726291.1 62414 31078 0.4979 0.7113
NW_003726292.1 61779 30802 0.4986 0.7475
NW_003726293.1 90840 41611 0.4581 0.7858
NW_003726294.1 61194 29584 0.4834 0.6841
NW_003726295.1 63245 31980 0.5057 0.7484
NW_003726296.1 60975 29884 0.4901 0.7038
NW_003726297.1 88336 39694 0.4494 0.7673
NW_003726298.1 62896 31122 0.4948 0.6766
NW_003726299.1 60346 28355 0.4699 0.6803
NW_003726300.1 70666 30844 0.4365 0.7059
NW_003726301.1 71007 42749 0.602 0.812
NW_003726302.1 59879 30174 0.5039 0.6999
NW_003726303.1 59817 29267 0.4893 0.7016
NW_003726304.1 66981 37063 0.5533 0.7652
NW_003726305.1 62805 31090 0.495 0.7011
NW_003726306.1 68857 32254 0.4684 0.6707
NW_003726307.1 58149 26635 0.458 0.7152
NW_003726308.1 84024 40352 0.4802 0.7985
NW_003726309.1 58658 29770 0.5075 0.701
NW_003726310.1 65402 32106 0.4909 0.7423
NW_003726311.1 56534 27811 0.4919 0.6787
NW_003726312.1 59023 28020 0.4747 0.71
NW_003726313.1 89903 35045 0.3898 0.7237
NW_003726314.1 54477 32463 0.5959 0.8552
NW_003726315.1 54307 26961 0.4965 0.6718
NW_003726316.1 69310 34298 0.4948 0.768
NW_003726317.1 57210 27785 0.4857 0.6903
NW_003726318.1 57907 31061 0.5364 0.7885
NW_003726319.1 53093 26909 0.5068 0.6864
NW_003726320.1 67358 29321 0.4353 0.6823
NW_003726321.1 54660 22443 0.4106 0.6667
NW_003726322.1 52548 26806 0.5101 0.7624
NW_003726323.1 52637 26938 0.5118 0.7305
NW_003726324.1 51964 26006 0.5005 0.7496
NW_003726325.1 51648 23336 0.4518 0.6885
NW_003726326.1 51582 26004 0.5041 0.7469
NW_003726327.1 52288 25997 0.4972 0.7378
NW_003726328.1 50462 24452 0.4846 0.705
NW_003726329.1 50869 26022 0.5115 0.7026
NW_003726330.1 53506 26806 0.501 0.7637
NW_003726331.1 50005 24112 0.4822 0.6787
NW_003726332.1 84691 37947 0.4481 0.794
NW_003726333.1 63256 30177 0.4771 0.7416
NW_003726334.1 59752 28729 0.4808 0.7647
NW_003726335.1 68739 28475 0.4142 0.7198
NW_003726336.1 49027 23605 0.4815 0.7137
NW_003726337.1 49032 25130 0.5125 0.7249
NW_003726338.1 57792 24376 0.4218 0.6643
NW_003726339.1 74646 29839 0.3997 0.6836
NW_003726340.1 48411 25383 0.5243 0.7108
NW_003726341.1 48200 24218 0.5024 0.7206
NW_003726342.1 75626 31406 0.4153 0.7008
NW_003726343.1 48436 24352 0.5028 0.7076
NW_003726344.1 47485 24217 0.51 0.7127
NW_003726345.1 52731 27218 0.5162 0.8082
NW_003726346.1 52367 26314 0.5025 0.7723
NW_003726347.1 46689 23583 0.5051 0.7533
NW_003726348.1 53681 28095 0.5234 0.7727
NW_003726349.1 73441 32284 0.4396 0.7616
NW_003726350.1 57620 25383 0.4405 0.719
NW_003726351.1 70154 31641 0.451 0.7668
NW_003726352.1 67100 31428 0.4684 0.7198
NW_003726353.1 48085 24506 0.5096 0.7469
NW_003726354.1 63970 31718 0.4958 0.7508
NW_003726355.1 45242 22452 0.4963 0.7412
NW_003726356.1 58859 23935 0.4066 0.6738
NW_003726357.1 45065 21222 0.4709 0.6529
NW_003726358.1 46098 24231 0.5256 0.7086
NW_003726359.1 70370 31349 0.4455 0.8064
NW_003726360.1 46044 22140 0.4808 0.7424
NW_003726361.1 45518 20010 0.4396 0.6788
NW_003726362.1 47960 23063 0.4809 0.7159
NW_003726363.1 44571 22101 0.4959 0.7599
NW_003726364.1 84617 39785 0.4702 0.8614
NW_003726365.1 51679 26004 0.5032 0.7266
NW_003726366.1 48264 23968 0.4966 0.7387
NW_003726367.1 50939 23587 0.463 0.7252
NW_003726368.1 72756 25143 0.3456 0.6424
NW_003726369.1 44216 23368 0.5285 0.6894
NW_003726370.1 43704 21758 0.4978 0.7304
NW_003726371.1 55991 22130 0.3952 0.6852
NW_003726372.1 54329 27473 0.5057 0.7889
NW_003726373.1 44549 23014 0.5166 0.6823
NW_003726374.1 44306 24625 0.5558 0.7321
NW_003726375.1 60428 24501 0.4055 0.6705
NW_003726376.1 42803 20599 0.4813 0.6995
NW_003726377.1 90666 39921 0.4403 0.8352
NW_003726378.1 42461 20611 0.4854 0.7235
NW_003726379.1 46059 22716 0.4932 0.6654
NW_003726380.1 58391 27478 0.4706 0.8624
NW_003726381.1 69503 28154 0.4051 0.7547
NW_003726382.1 41842 20266 0.4843 0.6859
NW_003726383.1 43189 23016 0.5329 0.7592
NW_003726384.1 42168 20616 0.4889 0.7361
NW_003726385.1 41454 19763 0.4767 0.6752
NW_003726386.1 43681 23007 0.5267 0.7358
NW_003726387.1 57311 29017 0.5063 0.7673
NW_003726388.1 68304 29338 0.4295 0.7221
NW_003726389.1 57240 28717 0.5017 0.8092
NW_003726390.1 42861 20878 0.4871 0.715
NW_003726391.1 43424 20074 0.4623 0.7099
NW_003726392.1 40931 19409 0.4742 0.7037
NW_003726393.1 41221 20910 0.5073 0.7492
NW_003726394.1 41006 23873 0.5822 0.8122
NW_003726395.1 40763 21188 0.5198 0.7602
NW_003726396.1 46509 21796 0.4686 0.705
NW_003726397.1 42743 17697 0.414 0.621
NW_003726398.1 40517 20053 0.4949 0.7025
NW_003726399.1 40818 21051 0.5157 0.7808
NW_003726400.1 45697 21611 0.4729 0.7409
NW_003726401.1 46980 22152 0.4715 0.7404
NW_003726402.1 42806 19972 0.4666 0.7169
NW_003726403.1 44573 23250 0.5216 0.7515
NW_003726404.1 39716 19752 0.4973 0.7154
NW_003726405.1 39345 22163 0.5633 0.7806
NW_003726406.1 46145 22742 0.4928 0.7318
NW_003726407.1 47441 22443 0.4731 0.7752
NW_003726408.1 39138 19375 0.495 0.7183
NW_003726409.1 40677 19134 0.4704 0.6569
NW_003726410.1 64983 31128 0.479 0.8375
NW_003726411.1 51094 22950 0.4492 0.7153
NW_003726412.1 38580 18229 0.4725 0.6382
NW_003726413.1 40054 20570 0.5136 0.704
NW_003726414.1 39199 21244 0.542 0.6834
NW_003726415.1 38084 21469 0.5637 0.7559
NW_003726416.1 41432 20940 0.5054 0.7739
NW_003726417.1 45027 21812 0.4844 0.6654
NW_003726418.1 37707 20045 0.5316 0.6974
NW_003726419.1 59547 26769 0.4495 0.7576
NW_003726420.1 58434 26067 0.4461 0.8207
NW_003726421.1 37389 17354 0.4641 0.665
NW_003726422.1 52308 22149 0.4234 0.696
NW_003726423.1 63560 29321 0.4613 0.8741
NW_003726424.1 69036 34963 0.5064 0.8433
NW_003726425.1 44261 20957 0.4735 0.7173
NW_003726426.1 50023 21786 0.4355 0.7091
NW_003726427.1 36777 18223 0.4955 0.719
NW_003726428.1 63789 25058 0.3928 0.7146
NW_003726429.1 56472 29003 0.5136 0.7568
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NW_003729169.1 4619 2688 0.5819 0.7791
NW_003729170.1 4613 2936 0.6365 0.7364
NW_003729171.1 4612 1786 0.3873 0.621
NW_003729172.1 4601 1791 0.3893 0.6714
NW_003729173.1 4600 2402 0.5222 0.8809
NW_003729174.1 4600 1499 0.3259 0.4953
NW_003729175.1 4594 2088 0.4545 0.6128
NW_003729176.1 4588 2097 0.4571 0.7388
NW_003729177.1 4580 2093 0.457 0.7029
NW_003729178.1 4577 2700 0.5899 0.8231
NW_003729179.1 4577 1496 0.3269 0.5708
NW_003729180.1 4577 2077 0.4538 0.6251
NW_003729181.1 4575 2394 0.5233 0.7046
NW_003729182.1 4574 2367 0.5175 0.6266
NW_003729183.1 4572 2387 0.5221 0.6743
NW_003729184.1 4572 2390 0.5227 0.8109
NW_003729185.1 4562 1799 0.3943 0.5439
NW_003729186.1 4555 2825 0.6202 0.9498
NW_003729187.1 4554 2683 0.5892 0.7073
NW_003729188.1 4552 2394 0.5259 0.774
NW_003729189.1 4550 2100 0.4615 0.5755
NW_003729190.1 4543 2679 0.5897 0.8368
NW_003729191.1 4541 2400 0.5285 0.595
NW_003729192.1 4539 2993 0.6594 1.0018
NW_003729193.1 4527 2698 0.596 0.7294
NW_003729194.1 4519 2094 0.4634 0.5537
NW_003729195.1 4507 2098 0.4655 0.6177
NW_003729196.1 4501 1487 0.3304 0.6196
NW_003729197.1 4485 2386 0.532 0.7059
NW_003729198.1 4480 2696 0.6018 0.7149
NW_003729199.1 4476 2389 0.5337 0.753
NW_003729200.1 4469 2076 0.4645 0.6236
NW_003729201.1 4463 2983 0.6684 0.9166
NW_003729202.1 4460 2092 0.4691 0.624
NW_003729203.1 4454 2690 0.604 0.8065
NW_003729204.1 4453 2389 0.5365 0.6727
NW_003729205.1 4447 2085 0.4689 0.6795
NW_003729206.1 4443 2692 0.6059 0.8544
NW_003729207.1 4439 2085 0.4697 0.6246
NW_003729208.1 4437 2093 0.4717 0.6843
NW_003729209.1 4430 889 0.2007 0.4578
NW_003729210.1 4429 1496 0.3378 0.5547
NW_003729211.1 4428 1481 0.3345 0.5496
NW_003729212.1 4420 1785 0.4038 0.5937
NW_003729213.1 4418 3131 0.7087 0.7423
NW_003729214.1 4418 2996 0.6781 0.7633
NW_003729215.1 4408 1200 0.2722 0.4694
NW_003729216.1 4404 1794 0.4074 0.6727
NW_003729217.1 4404 1480 0.3361 0.6604
NW_003729218.1 4403 2100 0.4769 0.6476
NW_003729219.1 4399 1451 0.3298 0.6538
NW_003729220.1 4393 1200 0.2732 0.4456
NW_003729221.1 4389 2364 0.5386 0.6782
NW_003729222.1 4389 2690 0.6129 0.8985
NW_003729223.1 4388 1473 0.3357 0.5389
NW_003729224.1 4378 2379 0.5434 0.888
NW_003729225.1 4368 1500 0.3434 0.4979
NW_003729226.1 4359 1483 0.3402 0.6235
NW_003729227.1 4356 2075 0.4764 0.5955
NW_003729228.1 4353 2087 0.4794 0.6406
NW_003729229.1 4329 2071 0.4784 0.8046
NW_003729230.1 4311 2525 0.5857 0.7787
NW_003729231.1 4302 1780 0.4138 0.5849
NW_003729232.1 4300 2088 0.4856 0.8
NW_003729233.1 4285 1787 0.417 0.6091
NW_003729234.1 4283 2692 0.6285 0.8172
NW_003729235.1 4282 1200 0.2802 0.4517
NW_003729236.1 4281 2400 0.5606 0.8439
NW_003729237.1 4279 1926 0.4501 0.6036
NW_003729238.1 4277 1493 0.3491 0.671
NW_003729239.1 4276 1782 0.4167 0.7478
NW_003729240.1 4276 1766 0.413 0.5841
NW_003729241.1 4252 2243 0.5275 0.7618
NW_003729242.1 4248 2060 0.4849 0.8009
NW_003729243.1 4239 2991 0.7056 0.8813
NW_003729244.1 4238 1500 0.3539 0.5815
NW_003729245.1 4234 2366 0.5588 0.648
NW_003729246.1 4233 2244 0.5301 0.7091
NW_003729247.1 4231 1795 0.4242 0.7683
NW_003729248.1 4225 2515 0.5953 0.7711
NW_003729249.1 4201 4018 0.9564 1.3479
NW_003729250.1 4198 2233 0.5319 0.8022
NW_003729251.1 4193 2087 0.4977 0.6596
NW_003729252.1 4186 1742 0.4161 0.6948
NW_003729253.1 4183 1500 0.3586 0.5936
NW_003729254.1 4177 1482 0.3548 0.5622
NW_003729255.1 4172 2400 0.5753 0.6712
NW_003729256.1 4163 2095 0.5032 0.6736
NW_003729257.1 4156 2063 0.4964 0.7639
NW_003729258.1 4141 3264 0.7882 0.9071
NW_003729259.1 4130 2082 0.5041 0.6708
NW_003729260.1 4130 2078 0.5031 0.7074
NW_003729261.1 4126 1745 0.4229 0.7823
NW_003729262.1 4123 2400 0.5821 0.7356
NW_003729263.1 4121 2690 0.6528 0.8154
NW_003729264.1 4117 1800 0.4372 0.6286
NW_003729265.1 4112 2977 0.724 1.0574
NW_003729266.1 4097 1489 0.3634 0.574
NW_003729267.1 4096 2096 0.5117 0.5602
NW_003729268.1 4070 2988 0.7342 0.8671
NW_003729269.1 4064 1799 0.4427 0.6435
NW_003729270.1 4061 600 0.1477 0.3548
NW_003729271.1 4060 3273 0.8062 0.7989
NW_003729272.1 4025 1347 0.3347 0.4719
NW_003729273.1 4025 2688 0.6678 0.7142
NW_003729274.1 4011 2090 0.5211 0.66
NW_003729275.1 4001 2084 0.5209 0.9219
NW_003729276.1 3976 1783 0.4484 0.6323
NW_003729277.1 3948 2068 0.5238 0.7239
NW_003729278.1 3941 1194 0.303 0.5013
NW_003729279.1 3928 1800 0.4582 0.8499
NW_003729280.1 3925 2073 0.5282 0.7784
NW_003729281.1 3919 2079 0.5305 0.7003
NW_003729282.1 3849 3128 0.8127 0.8316
NW_003729283.1 3848 2083 0.5413 0.7305
NW_003729284.1 3847 1499 0.3897 0.6394
NW_003729285.1 3817 2087 0.5468 0.7238
NW_003729286.1 3780 1495 0.3955 0.7056
NW_003729287.1 3780 2087 0.5521 0.7039
NW_003729288.1 3777 600 0.1589 0.3655
NW_003729289.1 3761 1176 0.3127 0.5413
NW_003729290.1 3750 2366 0.6309 0.8553
NW_003729291.1 3733 899 0.2408 0.4276
NW_003729292.1 3719 1473 0.3961 0.6472
NW_003729293.1 3718 1776 0.4777 0.7023
NW_003729294.1 3706 1770 0.4776 0.7865
NW_003729295.1 3700 1200 0.3243 0.5314
NW_003729296.1 3695 1346 0.3643 0.6526
NW_003729297.1 3652 1943 0.532 0.7873
NW_003729298.1 3649 1778 0.4873 0.7089
NW_003729299.1 3629 2090 0.5759 0.792
NW_003729300.1 3622 1935 0.5342 0.8233
NW_003729301.1 3616 900 0.2489 0.4905
NW_003729302.1 3614 1488 0.4117 0.5741
NW_003729303.1 3595 2399 0.6673 0.6269
NW_003729304.1 3589 2366 0.6592 0.8459
NW_003729305.1 3585 2032 0.5668 0.6907
NW_003729306.1 3580 1773 0.4953 0.7985
NW_003729307.1 3576 2086 0.5833 0.7867
NW_003729308.1 3564 1479 0.415 0.6176
NW_003729309.1 3524 2095 0.5945 0.794
NW_003729310.1 3506 1337 0.3813 0.5614
NW_003729311.1 3484 1198 0.3439 0.6141
NW_003729312.1 3480 1189 0.3417 0.7084
NW_003729313.1 3479 1494 0.4294 0.7024
NW_003729314.1 3440 2984 0.8674 1.0215
NW_003729315.1 3431 1186 0.3457 0.4756
NW_003729316.1 3430 1788 0.5213 0.876
NW_003729317.1 3407 1171 0.3437 0.5548
NW_003729318.1 3398 1650 0.4856 0.5394
NW_003729319.1 3393 1798 0.5299 0.7064
NW_003729320.1 3388 1500 0.4427 0.6689
NW_003729321.1 3369 1494 0.4435 0.8411
NW_003729322.1 3338 1781 0.5336 0.6687
NW_003729323.1 3331 1791 0.5377 0.8966
NW_003729324.1 3271 1771 0.5414 0.6972
NW_003729325.1 3257 1192 0.366 0.5462
NW_003729326.1 3257 1495 0.459 0.597
NW_003729327.1 3231 1487 0.4602 0.6589
NW_003729328.1 3135 1497 0.4775 0.9311
NW_003729329.1 3134 2081 0.664 0.5997
NW_003729330.1 3059 1790 0.5852 0.9572
NW_003729331.1 3011 1480 0.4915 0.6532
NW_003729332.1 2997 600 0.2002 0.4213
NW_003729333.1 2955 1480 0.5008 0.6337
NW_003729334.1 2933 596 0.2032 0.5006
NW_003729335.1 2850 1480 0.5193 0.8664
NW_003729336.1 2823 2069 0.7329 0.9
NW_003729337.1 2809 1783 0.6347 0.7383
NW_003729338.1 2772 295 0.1064 0.3084
NW_003729339.1 2729 1496 0.5482 0.7329
NW_003729340.1 2708 897 0.3312 0.4707
NW_003729341.1 2700 900 0.3333 0.5863
NW_003729342.1 2641 1200 0.4544 0.6373
NW_003729343.1 2494 1048 0.4202 0.7427
NW_003729344.1 2361 1500 0.6353 0.7877
NW_003729345.1 2327 1193 0.5127 0.6735
NW_003729346.1 2250 1178 0.5236 0.7886
NW_003729347.1 2145 900 0.4196 0.5673
NW_003729348.1 2046 896 0.4379 0.5906
NW_003729349.1 1999 900 0.4502 0.6185
NW_003729350.1 1819 894 0.4915 0.5391
NW_003729351.1 1790 298 0.1665 0.3725
NW_003729352.1 1685 900 0.5341 0.5944
NW_003729353.1 1573 281 0.1786 0.3831
NW_003729354.1 1115 1491 1.3372 1.1991
NC_002008.4 16727 8391 0.5016 0.6916

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 17:33:06
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