Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/1X_med_error_no_variance/alignment/1X_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/1X_med_error_no_variance/1X_med_error_no_variance_R1.fa results/1X_med_error_no_variance/1X_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 17:25:21 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/1X_med_error_no_variance/alignment/1X_med_error_no_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 16,073,088
Mapped reads 16,073,088 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 16,073,088 / 100%
Mapped reads, first in pair 8,036,544 / 50%
Mapped reads, second in pair 8,036,544 / 50%
Mapped reads, both in pair 16,073,088 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Supplementary alignments 2 / 0%
Read min/max/mean length 63 / 150 / 150
Duplicated reads (estimated) 54,341 / 0.34%
Duplication rate 0.34%
Clipped reads 38,417 / 0.24%

ACGT Content

Number/percentage of A's 707,584,103 / 29.35%
Number/percentage of C's 499,831,517 / 20.73%
Number/percentage of T's 705,588,316 / 29.27%
Number/percentage of G's 497,785,218 / 20.65%
Number/percentage of N's 4,245 / 0%
GC Percentage 41.38%

Coverage

Mean 0.9999
Standard Deviation 1.0196

Mapping Quality

Mean Mapping Quality 32.02

Insert size

Mean 351.92
Standard Deviation 4,301.35
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 1%
Mismatches 24,034,973
Insertions 427
Mapped reads with at least one insertion 0%
Deletions 343
Mapped reads with at least one deletion 0%
Homopolymer indels 27.01%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 122819334 1.0011 1.0175
NC_006584.3 85426708 85700050 1.0032 1.0197
NC_006585.3 91889043 91965808 1.0008 1.0157
NC_006586.3 88276631 88387480 1.0013 1.0176
NC_006587.3 88915250 88954530 1.0004 1.0169
NC_006588.3 77573801 77615453 1.0005 1.0178
NC_006589.3 80974532 81027023 1.0006 1.0168
NC_006590.3 74330416 74332663 1 1.0177
NC_006591.3 61074082 61187160 1.0019 1.0204
NC_006592.3 69331447 69323817 0.9999 1.0173
NC_006593.3 74389097 74399281 1.0001 1.0162
NC_006594.3 72498081 72490780 0.9999 1.0176
NC_006595.3 63241923 63239942 1 1.0171
NC_006596.3 60966679 60978468 1.0002 1.0177
NC_006597.3 64190966 64181292 0.9998 1.0182
NC_006598.3 59632846 59729641 1.0016 1.0205
NC_006599.3 64289059 64314258 1.0004 1.0171
NC_006600.3 55844845 55863800 1.0003 1.018
NC_006601.3 53741614 53734259 0.9999 1.016
NC_006602.3 58134056 58125289 0.9998 1.0191
NC_006603.3 50858623 50850601 0.9998 1.0161
NC_006604.3 61439934 61427729 0.9998 1.0132
NC_006605.3 52294480 52260408 0.9993 1.013
NC_006606.3 47698779 47702662 1.0001 1.0168
NC_006607.3 51628933 51618081 0.9998 1.0152
NC_006608.3 38964690 39007652 1.0011 1.0193
NC_006609.3 45876710 45833846 0.9991 1.0181
NC_006610.3 41182112 41169556 0.9997 1.0182
NC_006611.3 41845238 41818332 0.9994 1.0141
NC_006612.3 40214260 40208150 0.9998 1.018
NC_006613.3 39895921 39884517 0.9997 1.0149
NC_006614.3 38810281 38801088 0.9998 1.0152
NC_006615.3 31377067 31374565 0.9999 1.016
NC_006616.3 42124431 42114500 0.9998 1.0179
NC_006617.3 26524999 26509677 0.9994 1.0159
NC_006618.3 30810995 30801577 0.9997 1.0157
NC_006619.3 30902991 30898287 0.9998 1.0183
NC_006620.3 23914537 23920654 1.0003 1.0201
NC_006621.3 123869142 123847786 0.9998 1.0172
NW_003726127.1 2660953 2662933 1.0007 1.0232
NW_003726128.1 1881673 1898551 1.009 1.0689
NW_003726129.1 1415205 1425795 1.0075 1.0666
NW_003726130.1 1067467 1067309 0.9999 1.0994
NW_003726131.1 866315 867099 1.0009 1.0087
NW_003726132.1 881102 893322 1.0139 1.0608
NW_003726133.1 822601 829414 1.0083 1.0567
NW_003726134.1 741967 747859 1.0079 1.029
NW_003726135.1 745551 744801 0.999 1.1167
NW_003726136.1 602611 602041 0.9991 1.0157
NW_003726137.1 573630 571169 0.9957 1.0507
NW_003726138.1 666183 666559 1.0006 1.1081
NW_003726139.1 557017 562162 1.0092 1.0746
NW_003726140.1 510604 507868 0.9946 0.9953
NW_003726141.1 497093 500067 1.006 1.0388
NW_003726142.1 492630 493742 1.0023 1.0407
NW_003726143.1 577062 579568 1.0043 1.153
NW_003726144.1 561270 555872 0.9904 1.1352
NW_003726145.1 407330 410212 1.0071 1.0129
NW_003726146.1 405216 407217 1.0049 1.0284
NW_003726147.1 508668 502458 0.9878 1.1317
NW_003726148.1 540093 536074 0.9926 1.2056
NW_003726149.1 448434 448591 1.0004 1.0908
NW_003726150.1 377800 379784 1.0053 1.0481
NW_003726151.1 384880 379173 0.9852 1.0817
NW_003726152.1 367143 366849 0.9992 1.0397
NW_003726153.1 399987 399570 0.999 1.0723
NW_003726154.1 376204 374661 0.9959 1.0382
NW_003726155.1 416178 408868 0.9824 1.1132
NW_003726156.1 365470 364469 0.9973 1.0621
NW_003726157.1 322752 329978 1.0224 1.0555
NW_003726158.1 320591 321563 1.003 1.0336
NW_003726159.1 310270 308675 0.9949 1.0393
NW_003726160.1 433650 421191 0.9713 1.1812
NW_003726161.1 273228 275682 1.009 1.0037
NW_003726162.1 281659 282247 1.0021 1.0395
NW_003726163.1 320442 326689 1.0195 1.1391
NW_003726164.1 265648 269085 1.0129 1.0156
NW_003726165.1 241365 243588 1.0092 1.0171
NW_003726166.1 234529 242072 1.0322 1.0449
NW_003726167.1 252720 260691 1.0315 1.0966
NW_003726168.1 254975 258561 1.0141 1.1087
NW_003726169.1 226053 229180 1.0138 1.0217
NW_003726170.1 223744 221347 0.9893 1.0426
NW_003726171.1 227140 228875 1.0076 1.0309
NW_003726172.1 219672 218083 0.9928 1.0291
NW_003726173.1 214597 213296 0.9939 0.9968
NW_003726174.1 386314 388164 1.0048 1.3787
NW_003726175.1 204342 209098 1.0233 1.0006
NW_003726176.1 201724 203396 1.0083 1.0778
NW_003726177.1 216332 212394 0.9818 1.0669
NW_003726178.1 200877 203391 1.0125 1.0007
NW_003726179.1 310654 299684 0.9647 1.2384
NW_003726180.1 200932 199462 0.9927 1.0076
NW_003726181.1 201410 199797 0.992 1.0361
NW_003726182.1 292533 292759 1.0008 1.2096
NW_003726183.1 192561 193486 1.0048 1.016
NW_003726184.1 210134 212089 1.0093 1.0627
NW_003726185.1 197844 201870 1.0203 1.0772
NW_003726186.1 196813 209370 1.0638 1.089
NW_003726187.1 180359 181777 1.0079 1.0337
NW_003726188.1 210247 197391 0.9389 1.0791
NW_003726189.1 177735 184188 1.0363 1.0134
NW_003726190.1 172100 178175 1.0353 1.077
NW_003726191.1 166866 170688 1.0229 1.0073
NW_003726192.1 164926 165291 1.0022 1.0274
NW_003726193.1 157598 159582 1.0126 1.0935
NW_003726194.1 143980 143994 1.0001 1.0099
NW_003726195.1 141074 139798 0.991 1.0204
NW_003726196.1 139526 137095 0.9826 0.9982
NW_003726197.1 142260 150284 1.0564 1.0449
NW_003726198.1 138160 141584 1.0248 1.0313
NW_003726199.1 142296 146076 1.0266 1.0822
NW_003726200.1 133119 132584 0.996 1.0426
NW_003726201.1 129748 129295 0.9965 1.0176
NW_003726202.1 125962 131988 1.0478 1.0267
NW_003726203.1 127429 126879 0.9957 1.0029
NW_003726204.1 128261 124619 0.9716 1.0028
NW_003726205.1 131872 131396 0.9964 1.0475
NW_003726206.1 133432 133195 0.9982 1.0903
NW_003726207.1 119670 128390 1.0729 1.1392
NW_003726208.1 144750 134391 0.9284 1.0688
NW_003726209.1 120779 121181 1.0033 1.038
NW_003726210.1 115952 112493 0.9702 1.0391
NW_003726211.1 118237 110388 0.9336 0.9683
NW_003726212.1 111908 113690 1.0159 1.0475
NW_003726213.1 117332 127021 1.0826 1.077
NW_003726214.1 111759 111895 1.0012 1.0035
NW_003726215.1 108801 116096 1.067 1.0573
NW_003726216.1 112014 114586 1.023 1.104
NW_003726217.1 106428 107387 1.009 1.0144
NW_003726218.1 104912 99895 0.9522 0.9712
NW_003726219.1 104646 106500 1.0177 0.9986
NW_003726220.1 103248 101398 0.9821 1.0367
NW_003726221.1 129482 125672 0.9706 1.1435
NW_003726222.1 118473 119396 1.0078 1.113
NW_003726223.1 99993 102595 1.026 1.0421
NW_003726224.1 109585 110400 1.0074 1.0001
NW_003726225.1 124049 116993 0.9431 1.0934
NW_003726226.1 99658 98092 0.9843 1.0588
NW_003726227.1 101741 101393 0.9966 1.0398
NW_003726228.1 97365 99898 1.026 1.0654
NW_003726229.1 94395 91792 0.9724 0.9868
NW_003726230.1 102992 101391 0.9845 1.0395
NW_003726231.1 95509 93896 0.9831 1.0716
NW_003726232.1 92047 94492 1.0266 1.0547
NW_003726233.1 87753 86692 0.9879 0.9822
NW_003726234.1 96536 93289 0.9664 1.0308
NW_003726235.1 86544 87600 1.0122 1.0088
NW_003726236.1 85476 84890 0.9931 0.9635
NW_003726237.1 110512 108587 0.9826 1.1753
NW_003726238.1 83291 81894 0.9832 1.0297
NW_003726239.1 82459 84287 1.0222 0.9864
NW_003726240.1 81605 85198 1.044 0.9874
NW_003726241.1 82380 83989 1.0195 1.0377
NW_003726242.1 102198 101388 0.9921 1.2036
NW_003726243.1 82108 80991 0.9864 1.0763
NW_003726244.1 87041 83997 0.965 1.0544
NW_003726245.1 79722 77092 0.967 1.0017
NW_003726246.1 230124 225893 0.9816 1.7168
NW_003726247.1 78357 78584 1.0029 1.0402
NW_003726248.1 256406 252275 0.9839 1.8052
NW_003726249.1 78050 80982 1.0376 1.0086
NW_003726250.1 81930 81595 0.9959 1.0651
NW_003726251.1 77100 78297 1.0155 1.0029
NW_003726252.1 77130 76487 0.9917 0.9401
NW_003726253.1 79078 80098 1.0129 1.0289
NW_003726254.1 90550 85800 0.9475 1.108
NW_003726255.1 82767 83989 1.0148 1.1346
NW_003726256.1 89070 84594 0.9497 1.1023
NW_003726257.1 97802 97196 0.9938 1.1625
NW_003726258.1 79712 79795 1.001 1.0345
NW_003726259.1 79581 76189 0.9574 1.0163
NW_003726260.1 73720 74397 1.0092 0.9926
NW_003726261.1 97799 100783 1.0305 1.1453
NW_003726262.1 73171 73496 1.0044 0.9977
NW_003726263.1 104732 103789 0.991 1.2033
NW_003726264.1 78935 74100 0.9387 1.0273
NW_003726265.1 72992 74688 1.0232 1.0722
NW_003726266.1 68721 70496 1.0258 1.0289
NW_003726267.1 73611 74228 1.0084 1.1115
NW_003726268.1 68272 67785 0.9929 1.0145
NW_003726269.1 79297 75884 0.957 1.0982
NW_003726270.1 84443 79475 0.9412 1.0263
NW_003726271.1 80679 75300 0.9333 1.0689
NW_003726272.1 68834 69893 1.0154 1.0348
NW_003726273.1 67496 67495 1 1.13
NW_003726274.1 66523 65390 0.983 0.9991
NW_003726275.1 67057 67200 1.0021 1.0214
NW_003726276.1 66195 66893 1.0105 1.0755
NW_003726277.1 87584 85305 0.974 1.2013
NW_003726278.1 84679 85787 1.0131 1.118
NW_003726279.1 65840 67496 1.0252 1.0109
NW_003726280.1 65696 68695 1.0456 0.9466
NW_003726281.1 66021 65696 0.9951 1.013
NW_003726282.1 67300 68992 1.0251 1.0471
NW_003726283.1 88153 84895 0.963 1.1618
NW_003726284.1 92437 87269 0.9441 1.1579
NW_003726285.1 70351 69895 0.9935 1.0839
NW_003726286.1 64646 67477 1.0438 1.0682
NW_003726287.1 69126 68700 0.9938 1.0205
NW_003726288.1 227674 207587 0.9118 1.7754
NW_003726289.1 64123 63595 0.9918 1.0644
NW_003726290.1 61944 61200 0.988 1.0113
NW_003726291.1 62414 62698 1.0046 1.0142
NW_003726292.1 61779 62696 1.0148 1.0554
NW_003726293.1 90840 86088 0.9477 1.2104
NW_003726294.1 61194 62696 1.0245 0.9636
NW_003726295.1 63245 59696 0.9439 1.0159
NW_003726296.1 60975 60598 0.9938 1.0565
NW_003726297.1 88336 79191 0.8965 1.1338
NW_003726298.1 62896 51900 0.8252 0.9823
NW_003726299.1 60346 57300 0.9495 1.0069
NW_003726300.1 70666 56397 0.7981 0.9315
NW_003726301.1 71007 73800 1.0393 1.1058
NW_003726302.1 59879 61200 1.0221 1.0713
NW_003726303.1 59817 64787 1.0831 1.1285
NW_003726304.1 66981 64185 0.9583 1.097
NW_003726305.1 62805 63590 1.0125 1.0709
NW_003726306.1 68857 67198 0.9759 1.1033
NW_003726307.1 58149 57600 0.9906 0.9658
NW_003726308.1 84024 79195 0.9425 1.1636
NW_003726309.1 58658 60415 1.03 0.9695
NW_003726310.1 65402 67491 1.0319 1.1274
NW_003726311.1 56534 53395 0.9445 0.9956
NW_003726312.1 59023 58795 0.9961 1.0131
NW_003726313.1 89903 70188 0.7807 1.1051
NW_003726314.1 54477 59386 1.0901 1.1291
NW_003726315.1 54307 54900 1.0109 0.9989
NW_003726316.1 69310 64797 0.9349 1.1817
NW_003726317.1 57210 59098 1.033 1.0984
NW_003726318.1 57907 56998 0.9843 1.1507
NW_003726319.1 53093 53700 1.0114 1.0721
NW_003726320.1 67358 60000 0.8908 1.1407
NW_003726321.1 54660 50993 0.9329 0.9928
NW_003726322.1 52548 50687 0.9646 1.0112
NW_003726323.1 52637 53092 1.0086 0.9578
NW_003726324.1 51964 53096 1.0218 1.0237
NW_003726325.1 51648 50700 0.9816 0.9897
NW_003726326.1 51582 54298 1.0527 1.0334
NW_003726327.1 52288 52786 1.0095 1.0297
NW_003726328.1 50462 47393 0.9392 0.958
NW_003726329.1 50869 47700 0.9377 1.0373
NW_003726330.1 53506 52498 0.9812 0.963
NW_003726331.1 50005 50392 1.0077 0.9945
NW_003726332.1 84691 72590 0.8571 1.2189
NW_003726333.1 63256 62395 0.9864 1.1398
NW_003726334.1 59752 58493 0.9789 1.1134
NW_003726335.1 68739 61500 0.8947 1.1748
NW_003726336.1 49027 50997 1.0402 0.9955
NW_003726337.1 49032 49497 1.0095 1.0039
NW_003726338.1 57792 52014 0.9 1.0791
NW_003726339.1 74646 61494 0.8238 1.1773
NW_003726340.1 48411 49200 1.0163 1.0335
NW_003726341.1 48200 46797 0.9709 0.9435
NW_003726342.1 75626 68393 0.9044 1.1914
NW_003726343.1 48436 49800 1.0282 1.0047
NW_003726344.1 47485 46200 0.9729 0.993
NW_003726345.1 52731 53092 1.0068 1.1208
NW_003726346.1 52367 51892 0.9909 1.0722
NW_003726347.1 46689 45897 0.983 0.9704
NW_003726348.1 53681 51000 0.9501 1.0322
NW_003726349.1 73441 66890 0.9108 1.2216
NW_003726350.1 57620 57895 1.0048 1.1198
NW_003726351.1 70154 64193 0.915 1.2683
NW_003726352.1 67100 62096 0.9254 1.1988
NW_003726353.1 48085 47100 0.9795 0.9943
NW_003726354.1 63970 64500 1.0083 1.1725
NW_003726355.1 45242 45296 1.0012 0.9998
NW_003726356.1 58859 54293 0.9224 1.0933
NW_003726357.1 45065 48600 1.0784 1.0546
NW_003726358.1 46098 43500 0.9436 1.0422
NW_003726359.1 70370 56691 0.8056 1.2181
NW_003726360.1 46044 46197 1.0033 0.9867
NW_003726361.1 45518 46500 1.0216 1.0672
NW_003726362.1 47960 50091 1.0444 1.1912
NW_003726363.1 44571 44691 1.0027 1.0171
NW_003726364.1 84617 73797 0.8721 1.2842
NW_003726365.1 51679 53997 1.0449 1.0958
NW_003726366.1 48264 50695 1.0504 1.1543
NW_003726367.1 50939 47985 0.942 1.1442
NW_003726368.1 72756 63595 0.8741 1.2765
NW_003726369.1 44216 48293 1.0922 1.0971
NW_003726370.1 43704 43500 0.9953 1.0697
NW_003726371.1 55991 58189 1.0393 1.2697
NW_003726372.1 54329 48886 0.8998 1.0603
NW_003726373.1 44549 44095 0.9898 1.0427
NW_003726374.1 44306 46198 1.0427 1.0718
NW_003726375.1 60428 52200 0.8638 1.129
NW_003726376.1 42803 42295 0.9881 1.0627
NW_003726377.1 90666 82464 0.9095 1.4139
NW_003726378.1 42461 43798 1.0315 0.9734
NW_003726379.1 46059 46500 1.0096 1.0798
NW_003726380.1 58391 55493 0.9504 1.1121
NW_003726381.1 69503 56979 0.8198 1.1571
NW_003726382.1 41842 44400 1.0611 0.9617
NW_003726383.1 43189 44994 1.0418 1.0239
NW_003726384.1 42168 41682 0.9885 1.0125
NW_003726385.1 41454 41400 0.9987 0.9706
NW_003726386.1 43681 42296 0.9683 1.0143
NW_003726387.1 57311 57900 1.0103 1.2138
NW_003726388.1 68304 56996 0.8344 1.1412
NW_003726389.1 57240 56096 0.98 1.2221
NW_003726390.1 42861 42000 0.9799 1.0677
NW_003726391.1 43424 43800 1.0087 1.076
NW_003726392.1 40931 40498 0.9894 1.0258
NW_003726393.1 41221 41390 1.0041 1.0265
NW_003726394.1 41006 42300 1.0316 1.0598
NW_003726395.1 40763 43500 1.0671 0.9679
NW_003726396.1 46509 48000 1.0321 1.1237
NW_003726397.1 42743 41395 0.9685 1.0864
NW_003726398.1 40517 40200 0.9922 0.9676
NW_003726399.1 40818 39300 0.9628 0.9712
NW_003726400.1 45697 46495 1.0175 1.1337
NW_003726401.1 46980 45000 0.9579 1.1122
NW_003726402.1 42806 40488 0.9458 1.0966
NW_003726403.1 44573 44095 0.9893 1.0639
NW_003726404.1 39716 39587 0.9968 0.9884
NW_003726405.1 39345 37200 0.9455 1.0175
NW_003726406.1 46145 46500 1.0077 1.0873
NW_003726407.1 47441 43796 0.9232 1.0962
NW_003726408.1 39138 41391 1.0576 1.1501
NW_003726409.1 40677 41095 1.0103 1.0484
NW_003726410.1 64983 64795 0.9971 1.3139
NW_003726411.1 51094 45590 0.8923 1.2176
NW_003726412.1 38580 36896 0.9564 1.0046
NW_003726413.1 40054 40497 1.0111 1.1012
NW_003726414.1 39199 41700 1.0638 1.1098
NW_003726415.1 38084 38691 1.0159 1.0041
NW_003726416.1 41432 42000 1.0137 1.0431
NW_003726417.1 45027 40196 0.8927 1.0616
NW_003726418.1 37707 42600 1.1298 0.9763
NW_003726419.1 59547 52193 0.8765 1.2133
NW_003726420.1 58434 49489 0.8469 1.1697
NW_003726421.1 37389 38992 1.0429 1.0213
NW_003726422.1 52308 48600 0.9291 1.1675
NW_003726423.1 63560 53095 0.8354 1.2467
NW_003726424.1 69036 63277 0.9166 1.2807
NW_003726425.1 44261 37800 0.854 1.0766
NW_003726426.1 50023 45300 0.9056 1.139
NW_003726427.1 36777 36900 1.0033 0.9679
NW_003726428.1 63789 63592 0.9969 1.3757
NW_003726429.1 56472 55479 0.9824 1.2499
NW_003726430.1 36805 36900 1.0026 1.0353
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NW_003729175.1 4594 5396 1.1746 1.1411
NW_003729176.1 4588 4500 0.9808 0.9106
NW_003729177.1 4580 5400 1.179 1.0566
NW_003729178.1 4577 4800 1.0487 0.9931
NW_003729179.1 4577 4796 1.0478 1.3948
NW_003729180.1 4577 4200 0.9176 0.8192
NW_003729181.1 4575 4500 0.9836 0.8329
NW_003729182.1 4574 2400 0.5247 0.9448
NW_003729183.1 4572 4195 0.9175 1.1319
NW_003729184.1 4572 4498 0.9838 1.0088
NW_003729185.1 4562 5400 1.1837 1.1244
NW_003729186.1 4555 5097 1.119 1.2392
NW_003729187.1 4554 7193 1.5795 1.3267
NW_003729188.1 4552 3900 0.8568 0.9178
NW_003729189.1 4550 4196 0.9222 0.8126
NW_003729190.1 4543 4200 0.9245 0.9062
NW_003729191.1 4541 4500 0.991 1.3676
NW_003729192.1 4539 4795 1.0564 1.1027
NW_003729193.1 4527 4491 0.992 0.9985
NW_003729194.1 4519 4500 0.9958 0.9161
NW_003729195.1 4507 5400 1.1981 1.082
NW_003729196.1 4501 3600 0.7998 0.9376
NW_003729197.1 4485 4496 1.0025 1.2808
NW_003729198.1 4480 4800 1.0714 0.9479
NW_003729199.1 4476 5400 1.2064 1.0979
NW_003729200.1 4469 5098 1.1407 1.157
NW_003729201.1 4463 5393 1.2084 0.9201
NW_003729202.1 4460 5079 1.1388 1.116
NW_003729203.1 4454 3600 0.8083 0.8936
NW_003729204.1 4453 4500 1.0106 0.8947
NW_003729205.1 4447 4200 0.9445 0.8477
NW_003729206.1 4443 5100 1.1479 1.1215
NW_003729207.1 4439 4500 1.0137 1.0053
NW_003729208.1 4437 5098 1.149 1.1644
NW_003729209.1 4430 5097 1.1506 1.1437
NW_003729210.1 4429 4496 1.0151 0.8353
NW_003729211.1 4428 4497 1.0156 1.0571
NW_003729212.1 4420 4500 1.0181 0.962
NW_003729213.1 4418 4495 1.0174 1.2435
NW_003729214.1 4418 3598 0.8144 0.9429
NW_003729215.1 4408 4800 1.0889 1.0677
NW_003729216.1 4404 4499 1.0216 0.9827
NW_003729217.1 4404 4200 0.9537 1.2138
NW_003729218.1 4403 4500 1.022 0.8635
NW_003729219.1 4399 3000 0.682 1.0006
NW_003729220.1 4393 3300 0.7512 0.8731
NW_003729221.1 4389 3898 0.8881 0.884
NW_003729222.1 4389 4200 0.9569 0.9609
NW_003729223.1 4388 4196 0.9562 0.8656
NW_003729224.1 4378 2997 0.6846 0.904
NW_003729225.1 4368 3300 0.7555 0.799
NW_003729226.1 4359 4500 1.0323 1.2121
NW_003729227.1 4356 3900 0.8953 1.0647
NW_003729228.1 4353 4200 0.9649 0.9443
NW_003729229.1 4329 4200 0.9702 1.1468
NW_003729230.1 4311 4495 1.0427 1.1034
NW_003729231.1 4302 4200 0.9763 0.9499
NW_003729232.1 4300 4800 1.1163 1.1408
NW_003729233.1 4285 3900 0.9102 0.9442
NW_003729234.1 4283 3900 0.9106 1.051
NW_003729235.1 4282 4200 0.9809 1.1313
NW_003729236.1 4281 3900 0.911 1.1887
NW_003729237.1 4279 4796 1.1208 0.9823
NW_003729238.1 4277 4800 1.1223 1.1529
NW_003729239.1 4276 4496 1.0514 1.1125
NW_003729240.1 4276 3000 0.7016 1.0111
NW_003729241.1 4252 4200 0.9878 0.8209
NW_003729242.1 4248 5700 1.3418 1.1473
NW_003729243.1 4239 3581 0.8448 1.1076
NW_003729244.1 4238 2996 0.7069 0.7866
NW_003729245.1 4234 4200 0.992 1.0766
NW_003729246.1 4233 5400 1.2757 1.098
NW_003729247.1 4231 3000 0.7091 0.8566
NW_003729248.1 4225 3894 0.9217 1.1969
NW_003729249.1 4201 3595 0.8557 0.9126
NW_003729250.1 4198 2997 0.7139 0.7075
NW_003729251.1 4193 3000 0.7155 0.7612
NW_003729252.1 4186 4498 1.0745 1.1436
NW_003729253.1 4183 4200 1.0041 1.0074
NW_003729254.1 4177 4197 1.0048 0.9445
NW_003729255.1 4172 3000 0.7191 0.7465
NW_003729256.1 4163 5100 1.2251 0.8952
NW_003729257.1 4156 4196 1.0096 0.9384
NW_003729258.1 4141 3000 0.7245 0.9985
NW_003729259.1 4130 4200 1.0169 0.8084
NW_003729260.1 4130 3600 0.8717 1.022
NW_003729261.1 4126 5700 1.3815 1.0688
NW_003729262.1 4123 3900 0.9459 0.87
NW_003729263.1 4121 3450 0.8372 0.9544
NW_003729264.1 4117 3900 0.9473 1.0799
NW_003729265.1 4112 5397 1.3125 1.1438
NW_003729266.1 4097 5690 1.3888 1.2578
NW_003729267.1 4096 4500 1.0986 1.2382
NW_003729268.1 4070 4797 1.1786 1.1243
NW_003729269.1 4064 3000 0.7382 1.0459
NW_003729270.1 4061 2700 0.6649 0.7888
NW_003729271.1 4060 3900 0.9606 0.9572
NW_003729272.1 4025 2400 0.5963 0.9915
NW_003729273.1 4025 3000 0.7453 0.8488
NW_003729274.1 4011 3000 0.7479 0.9169
NW_003729275.1 4001 4495 1.1235 1.1187
NW_003729276.1 3976 3300 0.83 0.8668
NW_003729277.1 3948 3300 0.8359 0.8988
NW_003729278.1 3941 3600 0.9135 0.8577
NW_003729279.1 3928 3295 0.8388 0.8396
NW_003729280.1 3925 3892 0.9916 0.7915
NW_003729281.1 3919 3000 0.7655 0.816
NW_003729282.1 3849 3900 1.0133 1.0854
NW_003729283.1 3848 3300 0.8576 0.899
NW_003729284.1 3847 3598 0.9353 1.0034
NW_003729285.1 3817 3900 1.0217 0.9802
NW_003729286.1 3780 2700 0.7143 0.945
NW_003729287.1 3780 2996 0.7926 1.0635
NW_003729288.1 3777 3300 0.8737 1.0792
NW_003729289.1 3761 3890 1.0343 1.1086
NW_003729290.1 3750 4498 1.1995 1.0282
NW_003729291.1 3733 3896 1.0437 0.9931
NW_003729292.1 3719 4500 1.21 0.9161
NW_003729293.1 3718 3000 0.8069 0.8103
NW_003729294.1 3706 3300 0.8904 0.9017
NW_003729295.1 3700 3300 0.8919 0.9368
NW_003729296.1 3695 2400 0.6495 0.7697
NW_003729297.1 3652 3600 0.9858 1.0623
NW_003729298.1 3649 3296 0.9033 0.7552
NW_003729299.1 3629 4500 1.24 0.8995
NW_003729300.1 3622 3900 1.0768 1.0394
NW_003729301.1 3616 3299 0.9123 1.3072
NW_003729302.1 3614 3299 0.9128 1.2369
NW_003729303.1 3595 3900 1.0848 1.0951
NW_003729304.1 3589 3300 0.9195 0.8747
NW_003729305.1 3585 3600 1.0042 0.7666
NW_003729306.1 3580 3451 0.964 0.7428
NW_003729307.1 3576 3591 1.0042 0.9411
NW_003729308.1 3564 3000 0.8418 0.8931
NW_003729309.1 3524 3600 1.0216 0.8294
NW_003729310.1 3506 3600 1.0268 0.898
NW_003729311.1 3484 4200 1.2055 0.9639
NW_003729312.1 3480 2697 0.775 1.0209
NW_003729313.1 3479 3300 0.9485 0.9801
NW_003729314.1 3440 4196 1.2198 1.1248
NW_003729315.1 3431 3599 1.049 0.9798
NW_003729316.1 3430 2700 0.7872 0.8057
NW_003729317.1 3407 3000 0.8805 0.7636
NW_003729318.1 3398 2400 0.7063 0.7503
NW_003729319.1 3393 3000 0.8842 0.9744
NW_003729320.1 3388 3300 0.974 0.9248
NW_003729321.1 3369 2692 0.7991 0.8368
NW_003729322.1 3338 2700 0.8089 0.9382
NW_003729323.1 3331 3300 0.9907 0.9744
NW_003729324.1 3271 4200 1.284 1.007
NW_003729325.1 3257 2700 0.829 1.0623
NW_003729326.1 3257 3300 1.0132 0.9675
NW_003729327.1 3231 3300 1.0214 0.9609
NW_003729328.1 3135 2700 0.8612 0.9292
NW_003729329.1 3134 3600 1.1487 1.5164
NW_003729330.1 3059 3000 0.9807 0.9683
NW_003729331.1 3011 3600 1.1956 1.1186
NW_003729332.1 2997 2395 0.7991 0.8147
NW_003729333.1 2955 3300 1.1168 0.8071
NW_003729334.1 2933 2700 0.9206 0.8982
NW_003729335.1 2850 3300 1.1579 0.857
NW_003729336.1 2823 3000 1.0627 0.9399
NW_003729337.1 2809 1800 0.6408 0.6794
NW_003729338.1 2772 2693 0.9715 0.8821
NW_003729339.1 2729 2700 0.9894 1.1202
NW_003729340.1 2708 1800 0.6647 0.6583
NW_003729341.1 2700 2400 0.8889 1.0489
NW_003729342.1 2641 2400 0.9087 0.8778
NW_003729343.1 2494 2100 0.842 0.8309
NW_003729344.1 2361 2396 1.0148 0.9061
NW_003729345.1 2327 2400 1.0314 1.148
NW_003729346.1 2250 1800 0.8 0.7905
NW_003729347.1 2145 2100 0.979 1.1575
NW_003729348.1 2046 2400 1.173 1.1227
NW_003729349.1 1999 1800 0.9005 1.2847
NW_003729350.1 1819 1500 0.8246 0.7787
NW_003729351.1 1790 900 0.5028 0.7487
NW_003729352.1 1685 1800 1.0682 0.8135
NW_003729353.1 1573 2400 1.5257 1.1026
NW_003729354.1 1115 900 0.8072 0.7679
NC_002008.4 16727 16800 1.0044 1.0912

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 17:25:21
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