Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/1X_no_error_low_variance/alignment/1X_no_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/1X_no_error_low_variance/1X_no_error_low_variance_R1.fa results/1X_no_error_low_variance/1X_no_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 17:21:59 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/1X_no_error_low_variance/alignment/1X_no_error_low_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
Read min/max/mean length 150 / 150 / 150
Duplicated reads (estimated) 54,720 / 0.34%
Duplication rate 0.34%
Clipped reads 6,746 / 0.04%

ACGT Content

Number/percentage of A's 707,491,642 / 29.35%
Number/percentage of C's 497,844,243 / 20.65%
Number/percentage of T's 707,590,113 / 29.35%
Number/percentage of G's 497,849,156 / 20.65%
Number/percentage of N's 3,989 / 0%
GC Percentage 41.3%

Coverage

Mean 1
Standard Deviation 1.0197

Mapping Quality

Mean Mapping Quality 32.45

Insert size

Mean 360.52
Standard Deviation 30,050.72
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 0.07%
Mismatches 1,532,536
Insertions 112,992
Mapped reads with at least one insertion 0.7%
Deletions 113,643
Mapped reads with at least one deletion 0.7%
Homopolymer indels 28.9%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 122754394 1.0006 1.018
NC_006584.3 85426708 85676182 1.0029 1.0208
NC_006585.3 91889043 91939568 1.0005 1.0152
NC_006586.3 88276631 88318880 1.0005 1.0175
NC_006587.3 88915250 88944373 1.0003 1.0175
NC_006588.3 77573801 77592011 1.0002 1.0172
NC_006589.3 80974532 80994553 1.0002 1.0174
NC_006590.3 74330416 74332741 1 1.0173
NC_006591.3 61074082 61182401 1.0018 1.0196
NC_006592.3 69331447 69331064 1 1.0183
NC_006593.3 74389097 74421176 1.0004 1.0164
NC_006594.3 72498081 72502273 1.0001 1.0161
NC_006595.3 63241923 63251654 1.0002 1.0161
NC_006596.3 60966679 60981687 1.0002 1.0175
NC_006597.3 64190966 64193747 1 1.0193
NC_006598.3 59632846 59750922 1.002 1.0206
NC_006599.3 64289059 64335258 1.0007 1.0166
NC_006600.3 55844845 55869304 1.0004 1.0189
NC_006601.3 53741614 53750719 1.0002 1.0147
NC_006602.3 58134056 58128297 0.9999 1.0187
NC_006603.3 50858623 50866939 1.0002 1.0158
NC_006604.3 61439934 61438112 1 1.0158
NC_006605.3 52294480 52282888 0.9998 1.0158
NC_006606.3 47698779 47707247 1.0002 1.0158
NC_006607.3 51628933 51627973 1 1.0173
NC_006608.3 38964690 39006965 1.0011 1.0176
NC_006609.3 45876710 45856645 0.9996 1.0169
NC_006610.3 41182112 41172543 0.9998 1.0162
NC_006611.3 41845238 41838025 0.9998 1.015
NC_006612.3 40214260 40211603 0.9999 1.0172
NC_006613.3 39895921 39887626 0.9998 1.0146
NC_006614.3 38810281 38794504 0.9996 1.0139
NC_006615.3 31377067 31386105 1.0003 1.0176
NC_006616.3 42124431 42117768 0.9998 1.0166
NC_006617.3 26524999 26526380 1.0001 1.0225
NC_006618.3 30810995 30803419 0.9998 1.0179
NC_006619.3 30902991 30902291 1 1.0166
NC_006620.3 23914537 23918647 1.0002 1.0176
NC_006621.3 123869142 123874302 1 1.0178
NW_003726127.1 2660953 2676625 1.0059 1.0324
NW_003726128.1 1881673 1879807 0.999 1.0556
NW_003726129.1 1415205 1417509 1.0016 1.0343
NW_003726130.1 1067467 1068298 1.0008 1.0874
NW_003726131.1 866315 873260 1.008 1.0229
NW_003726132.1 881102 885874 1.0054 1.0614
NW_003726133.1 822601 837010 1.0175 1.0562
NW_003726134.1 741967 742502 1.0007 1.0081
NW_003726135.1 745551 746701 1.0015 1.1278
NW_003726136.1 602611 602098 0.9991 1.0244
NW_003726137.1 573630 574210 1.001 1.0228
NW_003726138.1 666183 669271 1.0046 1.1065
NW_003726139.1 557017 561626 1.0083 1.0448
NW_003726140.1 510604 514178 1.007 1.0187
NW_003726141.1 497093 508484 1.0229 1.0425
NW_003726142.1 492630 487476 0.9895 1.0329
NW_003726143.1 577062 575705 0.9976 1.1515
NW_003726144.1 561270 556202 0.991 1.1373
NW_003726145.1 407330 414877 1.0185 1.0298
NW_003726146.1 405216 412942 1.0191 1.0485
NW_003726147.1 508668 508793 1.0002 1.1485
NW_003726148.1 540093 533722 0.9882 1.198
NW_003726149.1 448434 450289 1.0041 1.1212
NW_003726150.1 377800 373192 0.9878 1.0348
NW_003726151.1 384880 380377 0.9883 1.0606
NW_003726152.1 367143 368393 1.0034 1.0498
NW_003726153.1 399987 402885 1.0072 1.0861
NW_003726154.1 376204 373479 0.9928 1.0723
NW_003726155.1 416178 414876 0.9969 1.1253
NW_003726156.1 365470 364943 0.9986 1.0594
NW_003726157.1 322752 328789 1.0187 1.0296
NW_003726158.1 320591 327582 1.0218 1.0554
NW_003726159.1 310270 310188 0.9997 1.0102
NW_003726160.1 433650 426875 0.9844 1.2048
NW_003726161.1 273228 274506 1.0047 1.0009
NW_003726162.1 281659 292491 1.0385 1.0678
NW_003726163.1 320442 320985 1.0017 1.0929
NW_003726164.1 265648 267883 1.0084 1.0335
NW_003726165.1 241365 244191 1.0117 1.0546
NW_003726166.1 234529 237000 1.0105 1.0019
NW_003726167.1 252720 261599 1.0351 1.0946
NW_003726168.1 254975 257095 1.0083 1.0916
NW_003726169.1 226053 224700 0.994 1.0214
NW_003726170.1 223744 226495 1.0123 1.0046
NW_003726171.1 227140 227997 1.0038 1.0407
NW_003726172.1 219672 221997 1.0106 1.0109
NW_003726173.1 214597 219892 1.0247 1.0421
NW_003726174.1 386314 386417 1.0003 1.3734
NW_003726175.1 204342 205196 1.0042 1.0204
NW_003726176.1 201724 205198 1.0172 1.0374
NW_003726177.1 216332 220504 1.0193 1.065
NW_003726178.1 200877 202505 1.0081 1.0223
NW_003726179.1 310654 304499 0.9802 1.2505
NW_003726180.1 200932 201895 1.0048 1.059
NW_003726181.1 201410 205811 1.0219 1.0412
NW_003726182.1 292533 273902 0.9363 1.1626
NW_003726183.1 192561 192593 1.0002 1.0142
NW_003726184.1 210134 214505 1.0208 1.0768
NW_003726185.1 197844 197390 0.9977 1.0776
NW_003726186.1 196813 203398 1.0335 1.0637
NW_003726187.1 180359 182994 1.0146 1.0086
NW_003726188.1 210247 203100 0.966 1.0651
NW_003726189.1 177735 182993 1.0296 1.0074
NW_003726190.1 172100 182696 1.0616 1.0171
NW_003726191.1 166866 172224 1.0321 1.0313
NW_003726192.1 164926 172515 1.046 1.0465
NW_003726193.1 157598 158077 1.003 1.0296
NW_003726194.1 143980 143999 1.0001 1.0592
NW_003726195.1 141074 142194 1.0079 1.0475
NW_003726196.1 139526 140994 1.0105 1.005
NW_003726197.1 142260 141898 0.9975 1.0243
NW_003726198.1 138160 138314 1.0011 1.0191
NW_003726199.1 142296 148203 1.0415 1.0427
NW_003726200.1 133119 132610 0.9962 1.0216
NW_003726201.1 129748 129287 0.9964 1.0098
NW_003726202.1 125962 124192 0.9859 1.0029
NW_003726203.1 127429 128095 1.0052 1.0334
NW_003726204.1 128261 129314 1.0082 1.0664
NW_003726205.1 131872 131981 1.0008 1.0921
NW_003726206.1 133432 138903 1.041 1.1034
NW_003726207.1 119670 121202 1.0128 1.0203
NW_003726208.1 144750 135903 0.9389 1.0879
NW_003726209.1 120779 120303 0.9961 1.066
NW_003726210.1 115952 120913 1.0428 1.0598
NW_003726211.1 118237 116997 0.9895 1.0352
NW_003726212.1 111908 111618 0.9974 0.9767
NW_003726213.1 117332 118211 1.0075 1.0507
NW_003726214.1 111759 111890 1.0012 1.0027
NW_003726215.1 108801 108006 0.9927 1.0225
NW_003726216.1 112014 118212 1.0553 1.067
NW_003726217.1 106428 111600 1.0486 1.0402
NW_003726218.1 104912 106788 1.0179 1.0077
NW_003726219.1 104646 101400 0.969 1.0161
NW_003726220.1 103248 105579 1.0226 0.9805
NW_003726221.1 129482 126911 0.9801 1.1542
NW_003726222.1 118473 118786 1.0026 1.1142
NW_003726223.1 99993 102295 1.023 0.9785
NW_003726224.1 109585 107704 0.9828 1.0526
NW_003726225.1 124049 120599 0.9722 1.0798
NW_003726226.1 99658 100223 1.0057 1.0249
NW_003726227.1 101741 101398 0.9966 1.0671
NW_003726228.1 97365 100805 1.0353 1.0137
NW_003726229.1 94395 95397 1.0106 1.0651
NW_003726230.1 102992 96304 0.9351 1.0331
NW_003726231.1 95509 92696 0.9705 1.0154
NW_003726232.1 92047 93299 1.0136 1.0412
NW_003726233.1 87753 89098 1.0153 1.0175
NW_003726234.1 96536 94798 0.982 1.0847
NW_003726235.1 86544 86702 1.0018 1.0312
NW_003726236.1 85476 86095 1.0072 1.0349
NW_003726237.1 110512 103489 0.9365 1.1434
NW_003726238.1 83291 82808 0.9942 0.9993
NW_003726239.1 82459 84602 1.026 1.0317
NW_003726240.1 81605 84894 1.0403 1.0027
NW_003726241.1 82380 83098 1.0087 1.0151
NW_003726242.1 102198 100503 0.9834 1.187
NW_003726243.1 82108 82198 1.0011 1.012
NW_003726244.1 87041 87011 0.9997 1.0855
NW_003726245.1 79722 78913 0.9899 1.0579
NW_003726246.1 230124 225600 0.9803 1.7523
NW_003726247.1 78357 78300 0.9993 1.0517
NW_003726248.1 256406 252633 0.9853 1.8244
NW_003726249.1 78050 79799 1.0224 1.0584
NW_003726250.1 81930 83403 1.018 1.0612
NW_003726251.1 77100 77402 1.0039 0.9779
NW_003726252.1 77130 78000 1.0113 0.9621
NW_003726253.1 79078 76497 0.9674 0.9911
NW_003726254.1 90550 90885 1.0037 1.0867
NW_003726255.1 82767 84292 1.0184 1.0794
NW_003726256.1 89070 76802 0.8623 1.013
NW_003726257.1 97802 97187 0.9937 1.2277
NW_003726258.1 79712 79785 1.0009 1.0664
NW_003726259.1 79581 84286 1.0591 1.0904
NW_003726260.1 73720 73787 1.0009 0.9833
NW_003726261.1 97799 95390 0.9754 1.1407
NW_003726262.1 73171 73808 1.0087 0.9572
NW_003726263.1 104732 99302 0.9482 1.111
NW_003726264.1 78935 73200 0.9273 1.0548
NW_003726265.1 72992 73796 1.011 1.0393
NW_003726266.1 68721 70801 1.0303 1.0045
NW_003726267.1 73611 69303 0.9415 1.0713
NW_003726268.1 68272 68405 1.0019 0.9963
NW_003726269.1 79297 79195 0.9987 1.0878
NW_003726270.1 84443 84307 0.9984 1.1494
NW_003726271.1 80679 77995 0.9667 1.1112
NW_003726272.1 68834 67190 0.9761 0.9974
NW_003726273.1 67496 67500 1.0001 1.0403
NW_003726274.1 66523 68092 1.0236 1.0425
NW_003726275.1 67057 67490 1.0065 1.04
NW_003726276.1 66195 65701 0.9925 1.0521
NW_003726277.1 87584 84297 0.9625 1.1533
NW_003726278.1 84679 82201 0.9707 1.1512
NW_003726279.1 65840 67496 1.0252 1.0588
NW_003726280.1 65696 66903 1.0184 1.0157
NW_003726281.1 66021 66600 1.0088 1.0976
NW_003726282.1 67300 66003 0.9807 1.0387
NW_003726283.1 88153 78903 0.8951 1.1167
NW_003726284.1 92437 90306 0.9769 1.2244
NW_003726285.1 70351 69297 0.985 1.0945
NW_003726286.1 64646 67197 1.0395 1.1172
NW_003726287.1 69126 67496 0.9764 1.0114
NW_003726288.1 227674 207295 0.9105 1.7881
NW_003726289.1 64123 63301 0.9872 1.0388
NW_003726290.1 61944 62702 1.0122 0.9724
NW_003726291.1 62414 63602 1.019 1.0132
NW_003726292.1 61779 62707 1.015 1.0692
NW_003726293.1 90840 86093 0.9477 1.2006
NW_003726294.1 61194 62108 1.0149 0.9836
NW_003726295.1 63245 61796 0.9771 0.967
NW_003726296.1 60975 59391 0.974 1.077
NW_003726297.1 88336 87301 0.9883 1.2298
NW_003726298.1 62896 56399 0.8967 0.995
NW_003726299.1 60346 59995 0.9942 1.0113
NW_003726300.1 70666 55499 0.7854 0.9527
NW_003726301.1 71007 73499 1.0351 1.1394
NW_003726302.1 59879 59393 0.9919 1.0085
NW_003726303.1 59817 62402 1.0432 0.9858
NW_003726304.1 66981 65099 0.9719 0.9817
NW_003726305.1 62805 62708 0.9985 1.0783
NW_003726306.1 68857 66601 0.9672 1.1362
NW_003726307.1 58149 60594 1.042 1.0557
NW_003726308.1 84024 81600 0.9712 1.2166
NW_003726309.1 58658 55494 0.9461 0.9491
NW_003726310.1 65402 65107 0.9955 1.1086
NW_003726311.1 56534 52193 0.9232 0.9871
NW_003726312.1 59023 57607 0.976 1.0726
NW_003726313.1 89903 65392 0.7274 1.0987
NW_003726314.1 54477 61207 1.1235 1.11
NW_003726315.1 54307 59400 1.0938 1.0185
NW_003726316.1 69310 68100 0.9825 1.1952
NW_003726317.1 57210 56695 0.991 1.1098
NW_003726318.1 57907 58500 1.0102 1.1009
NW_003726319.1 53093 50994 0.9605 0.9632
NW_003726320.1 67358 58199 0.864 1.0269
NW_003726321.1 54660 58497 1.0702 1.023
NW_003726322.1 52548 51294 0.9761 0.9793
NW_003726323.1 52637 50702 0.9632 1.0149
NW_003726324.1 51964 51014 0.9817 1.0001
NW_003726325.1 51648 56098 1.0862 1.0394
NW_003726326.1 51582 50990 0.9885 1.0638
NW_003726327.1 52288 57601 1.1016 1.0582
NW_003726328.1 50462 48600 0.9631 0.9117
NW_003726329.1 50869 56999 1.1205 1.0794
NW_003726330.1 53506 51602 0.9644 1.0863
NW_003726331.1 50005 50099 1.0019 1.0148
NW_003726332.1 84691 65103 0.7687 1.0701
NW_003726333.1 63256 59406 0.9391 1.1341
NW_003726334.1 59752 59107 0.9892 1.1552
NW_003726335.1 68739 56391 0.8204 1.0976
NW_003726336.1 49027 49198 1.0035 0.9751
NW_003726337.1 49032 50095 1.0217 1.0398
NW_003726338.1 57792 57315 0.9917 1.1296
NW_003726339.1 74646 60588 0.8117 1.1116
NW_003726340.1 48411 49498 1.0225 1.0067
NW_003726341.1 48200 45001 0.9336 0.9484
NW_003726342.1 75626 70194 0.9282 1.1847
NW_003726343.1 48436 48903 1.0096 0.9726
NW_003726344.1 47485 46191 0.9727 1.0025
NW_003726345.1 52731 52502 0.9957 1.0949
NW_003726346.1 52367 53404 1.0198 1.0906
NW_003726347.1 46689 48300 1.0345 1.013
NW_003726348.1 53681 53399 0.9947 1.0701
NW_003726349.1 73441 63602 0.866 1.153
NW_003726350.1 57620 52802 0.9164 1.1239
NW_003726351.1 70154 65397 0.9322 1.24
NW_003726352.1 67100 59401 0.8853 1.1635
NW_003726353.1 48085 47697 0.9919 0.977
NW_003726354.1 63970 63888 0.9987 1.1812
NW_003726355.1 45242 45000 0.9947 1.0225
NW_003726356.1 58859 46797 0.7951 1.0531
NW_003726357.1 45065 39598 0.8787 0.9574
NW_003726358.1 46098 44697 0.9696 1.0297
NW_003726359.1 70370 59093 0.8397 1.1622
NW_003726360.1 46044 47088 1.0227 0.9508
NW_003726361.1 45518 44406 0.9756 1.0193
NW_003726362.1 47960 50102 1.0447 1.0693
NW_003726363.1 44571 44701 1.0029 1.032
NW_003726364.1 84617 78000 0.9218 1.3661
NW_003726365.1 51679 52501 1.0159 1.0424
NW_003726366.1 48264 46210 0.9574 0.9952
NW_003726367.1 50939 52502 1.0307 1.1313
NW_003726368.1 72756 62998 0.8659 1.1923
NW_003726369.1 44216 45310 1.0247 1.1423
NW_003726370.1 43704 43804 1.0023 0.9906
NW_003726371.1 55991 54292 0.9697 1.1222
NW_003726372.1 54329 46191 0.8502 1.0353
NW_003726373.1 44549 45595 1.0235 1.0078
NW_003726374.1 44306 44099 0.9953 1.0834
NW_003726375.1 60428 50100 0.8291 1.0627
NW_003726376.1 42803 43794 1.0232 1.0225
NW_003726377.1 90666 87601 0.9662 1.4747
NW_003726378.1 42461 45001 1.0598 1.0341
NW_003726379.1 46059 45003 0.9771 1.011
NW_003726380.1 58391 56399 0.9659 1.1382
NW_003726381.1 69503 56100 0.8072 1.1008
NW_003726382.1 41842 43500 1.0396 1.0358
NW_003726383.1 43189 44702 1.035 1.1066
NW_003726384.1 42168 43195 1.0244 1.1002
NW_003726385.1 41454 42597 1.0276 0.9934
NW_003726386.1 43681 43492 0.9957 1.0127
NW_003726387.1 57311 57007 0.9947 1.2202
NW_003726388.1 68304 60901 0.8916 1.1894
NW_003726389.1 57240 56696 0.9905 1.1485
NW_003726390.1 42861 45894 1.0708 1.0645
NW_003726391.1 43424 45307 1.0434 1.0365
NW_003726392.1 40931 41402 1.0115 1.0218
NW_003726393.1 41221 39002 0.9462 0.9854
NW_003726394.1 41006 41101 1.0023 0.9833
NW_003726395.1 40763 43502 1.0672 1.1395
NW_003726396.1 46509 42900 0.9224 1.0002
NW_003726397.1 42743 43198 1.0106 1.0601
NW_003726398.1 40517 41398 1.0217 0.977
NW_003726399.1 40818 40492 0.992 0.9876
NW_003726400.1 45697 45901 1.0045 1.0944
NW_003726401.1 46980 43202 0.9196 1.0932
NW_003726402.1 42806 44702 1.0443 1.1122
NW_003726403.1 44573 45302 1.0164 1.1554
NW_003726404.1 39716 39599 0.9971 1.0966
NW_003726405.1 39345 37507 0.9533 0.8873
NW_003726406.1 46145 45899 0.9947 1.0688
NW_003726407.1 47441 45302 0.9549 1.0608
NW_003726408.1 39138 39006 0.9966 1.0093
NW_003726409.1 40677 41406 1.0179 1.0619
NW_003726410.1 64983 63003 0.9695 1.328
NW_003726411.1 51094 47401 0.9277 1.1368
NW_003726412.1 38580 38094 0.9874 1.0253
NW_003726413.1 40054 39603 0.9887 0.9466
NW_003726414.1 39199 44699 1.1403 1.0643
NW_003726415.1 38084 43505 1.1423 1.0708
NW_003726416.1 41432 41400 0.9992 1.0926
NW_003726417.1 45027 43799 0.9727 1.1521
NW_003726418.1 37707 42304 1.1219 1.0898
NW_003726419.1 59547 56701 0.9522 1.2211
NW_003726420.1 58434 54887 0.9393 1.2944
NW_003726421.1 37389 38099 1.019 0.9634
NW_003726422.1 52308 44993 0.8602 1.1618
NW_003726423.1 63560 58802 0.9251 1.2784
NW_003726424.1 69036 61798 0.8952 1.3243
NW_003726425.1 44261 36000 0.8134 1.0084
NW_003726426.1 50023 48291 0.9654 1.2073
NW_003726427.1 36777 37779 1.0272 1.0998
NW_003726428.1 63789 62699 0.9829 1.3382
NW_003726429.1 56472 54305 0.9616 1.2885
NW_003726430.1 36805 36300 0.9863 1.1222
NW_003726431.1 36868 38704 1.0498 1.1188
NW_003726432.1 37334 34197 0.916 0.9809
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NW_003729179.1 4577 4200 0.9176 0.877
NW_003729180.1 4577 3900 0.8521 0.9777
NW_003729181.1 4575 4800 1.0492 1.0302
NW_003729182.1 4574 3300 0.7215 0.8696
NW_003729183.1 4572 5100 1.1155 1.1987
NW_003729184.1 4572 4500 0.9843 0.9999
NW_003729185.1 4562 4500 0.9864 1.0885
NW_003729186.1 4555 5100 1.1196 1.0295
NW_003729187.1 4554 5700 1.2516 1.0724
NW_003729188.1 4552 3300 0.725 1.0219
NW_003729189.1 4550 4800 1.0549 0.9952
NW_003729190.1 4543 6000 1.3207 1.0649
NW_003729191.1 4541 4500 0.991 1.1787
NW_003729192.1 4539 5100 1.1236 0.9185
NW_003729193.1 4527 3600 0.7952 0.7679
NW_003729194.1 4519 3900 0.863 0.8462
NW_003729195.1 4507 5099 1.1314 1.0536
NW_003729196.1 4501 4800 1.0664 1.0056
NW_003729197.1 4485 4499 1.0031 0.8663
NW_003729198.1 4480 4500 1.0045 1.0314
NW_003729199.1 4476 4796 1.0715 1.1402
NW_003729200.1 4469 4800 1.0741 0.948
NW_003729201.1 4463 3901 0.8741 0.8726
NW_003729202.1 4460 4800 1.0762 1.2233
NW_003729203.1 4454 4200 0.943 1.114
NW_003729204.1 4453 3600 0.8084 0.9734
NW_003729205.1 4447 4500 1.0119 0.8654
NW_003729206.1 4443 3900 0.8778 0.8756
NW_003729207.1 4439 4500 1.0137 0.8925
NW_003729208.1 4437 4498 1.0137 1.249
NW_003729209.1 4430 6600 1.4898 1.3057
NW_003729210.1 4429 6600 1.4902 1.3958
NW_003729211.1 4428 4500 1.0163 1.1544
NW_003729212.1 4420 6300 1.4253 1.1564
NW_003729213.1 4418 4501 1.0188 0.9482
NW_003729214.1 4418 5401 1.2225 1.1888
NW_003729215.1 4408 3303 0.7493 1.038
NW_003729216.1 4404 4499 1.0216 0.939
NW_003729217.1 4404 4200 0.9537 0.816
NW_003729218.1 4403 4500 1.022 0.9415
NW_003729219.1 4399 4500 1.023 0.9532
NW_003729220.1 4393 4200 0.9561 1.0011
NW_003729221.1 4389 4498 1.0248 1.309
NW_003729222.1 4389 6901 1.5723 1.085
NW_003729223.1 4388 4500 1.0255 1.0085
NW_003729224.1 4378 4196 0.9584 1.159
NW_003729225.1 4368 3300 0.7555 0.839
NW_003729226.1 4359 4200 0.9635 0.9331
NW_003729227.1 4356 5100 1.1708 1.1625
NW_003729228.1 4353 5099 1.1714 0.986
NW_003729229.1 4329 3900 0.9009 0.9102
NW_003729230.1 4311 4501 1.0441 1.103
NW_003729231.1 4302 4500 1.046 0.8972
NW_003729232.1 4300 4200 0.9767 0.9906
NW_003729233.1 4285 3600 0.8401 0.9642
NW_003729234.1 4283 4200 0.9806 0.8992
NW_003729235.1 4282 3000 0.7006 0.6933
NW_003729236.1 4281 3000 0.7008 1.0008
NW_003729237.1 4279 5100 1.1919 1.1347
NW_003729238.1 4277 3899 0.9116 0.8238
NW_003729239.1 4276 3600 0.8419 0.9632
NW_003729240.1 4276 2700 0.6314 0.9054
NW_003729241.1 4252 3599 0.8464 0.9617
NW_003729242.1 4248 3901 0.9183 0.8338
NW_003729243.1 4239 3897 0.9193 0.8491
NW_003729244.1 4238 3000 0.7079 0.8143
NW_003729245.1 4234 4200 0.992 0.9912
NW_003729246.1 4233 4499 1.0628 1.1996
NW_003729247.1 4231 4800 1.1345 1.2033
NW_003729248.1 4225 2100 0.497 0.8541
NW_003729249.1 4201 4800 1.1426 1.1022
NW_003729250.1 4198 3000 0.7146 0.8864
NW_003729251.1 4193 3600 0.8586 0.9405
NW_003729252.1 4186 4200 1.0033 1.0988
NW_003729253.1 4183 3600 0.8606 0.9972
NW_003729254.1 4177 3900 0.9337 0.7353
NW_003729255.1 4172 5100 1.2224 1.116
NW_003729256.1 4163 4498 1.0805 0.9494
NW_003729257.1 4156 4200 1.0106 1.0074
NW_003729258.1 4141 3900 0.9418 0.9908
NW_003729259.1 4130 4200 1.0169 0.8926
NW_003729260.1 4130 3299 0.7988 0.9745
NW_003729261.1 4126 5101 1.2363 1.0034
NW_003729262.1 4123 4800 1.1642 0.9396
NW_003729263.1 4121 4199 1.0189 0.9111
NW_003729264.1 4117 4192 1.0182 1.3594
NW_003729265.1 4112 3297 0.8018 0.8963
NW_003729266.1 4097 3900 0.9519 1.0201
NW_003729267.1 4096 4200 1.0254 1.0736
NW_003729268.1 4070 4200 1.0319 0.9215
NW_003729269.1 4064 3600 0.8858 0.9564
NW_003729270.1 4061 3300 0.8126 0.8512
NW_003729271.1 4060 4200 1.0345 1.0683
NW_003729272.1 4025 3600 0.8944 0.8677
NW_003729273.1 4025 3600 0.8944 0.9653
NW_003729274.1 4011 4200 1.0471 0.9221
NW_003729275.1 4001 3300 0.8248 1.1477
NW_003729276.1 3976 3300 0.83 0.9443
NW_003729277.1 3948 3900 0.9878 1.1282
NW_003729278.1 3941 4804 1.219 1.0345
NW_003729279.1 3928 2700 0.6874 0.8751
NW_003729280.1 3925 4200 1.0701 1.0621
NW_003729281.1 3919 3602 0.9191 0.9594
NW_003729282.1 3849 4200 1.0912 1.3535
NW_003729283.1 3848 3901 1.0138 1.1004
NW_003729284.1 3847 3300 0.8578 1.0147
NW_003729285.1 3817 3000 0.786 0.9199
NW_003729286.1 3780 3600 0.9524 0.8309
NW_003729287.1 3780 3300 0.873 1.1589
NW_003729288.1 3777 4200 1.112 1.1202
NW_003729289.1 3761 4201 1.117 0.7013
NW_003729290.1 3750 2700 0.72 0.7866
NW_003729291.1 3733 3900 1.0447 1.2833
NW_003729292.1 3719 2702 0.7265 0.8153
NW_003729293.1 3718 3904 1.05 0.8189
NW_003729294.1 3706 3900 1.0523 1.2534
NW_003729295.1 3700 2400 0.6486 0.7667
NW_003729296.1 3695 3900 1.0555 1.189
NW_003729297.1 3652 3599 0.9855 0.9443
NW_003729298.1 3649 3900 1.0688 1.055
NW_003729299.1 3629 2400 0.6613 0.8103
NW_003729300.1 3622 3600 0.9939 0.8592
NW_003729301.1 3616 2700 0.7467 0.9014
NW_003729302.1 3614 3000 0.8301 1.0684
NW_003729303.1 3595 4498 1.2512 0.9511
NW_003729304.1 3589 3300 0.9195 0.7344
NW_003729305.1 3585 3600 1.0042 0.8599
NW_003729306.1 3580 3900 1.0894 1.166
NW_003729307.1 3576 3900 1.0906 0.7937
NW_003729308.1 3564 3300 0.9259 1.1608
NW_003729309.1 3524 4200 1.1918 1.0316
NW_003729310.1 3506 3600 1.0268 0.738
NW_003729311.1 3484 3000 0.8611 1.188
NW_003729312.1 3480 3000 0.8621 0.8008
NW_003729313.1 3479 3603 1.0356 0.9779
NW_003729314.1 3440 3600 1.0465 0.8939
NW_003729315.1 3431 3600 1.0493 1.0906
NW_003729316.1 3430 3901 1.1373 1.1655
NW_003729317.1 3407 3000 0.8805 0.8736
NW_003729318.1 3398 2400 0.7063 0.7316
NW_003729319.1 3393 3000 0.8842 1.0938
NW_003729320.1 3388 3300 0.974 1.2116
NW_003729321.1 3369 2400 0.7124 0.7104
NW_003729322.1 3338 2999 0.8984 0.8748
NW_003729323.1 3331 3301 0.991 1.1041
NW_003729324.1 3271 3300 1.0089 1.1733
NW_003729325.1 3257 2400 0.7369 1.024
NW_003729326.1 3257 3301 1.0135 1.006
NW_003729327.1 3231 3900 1.2071 1.2108
NW_003729328.1 3135 2098 0.6692 0.7927
NW_003729329.1 3134 1800 0.5743 0.8507
NW_003729330.1 3059 3299 1.0785 0.8926
NW_003729331.1 3011 2100 0.6974 0.8254
NW_003729332.1 2997 3600 1.2012 1.4699
NW_003729333.1 2955 2701 0.914 1.1054
NW_003729334.1 2933 2700 0.9206 0.9838
NW_003729335.1 2850 2700 0.9474 1.1142
NW_003729336.1 2823 3900 1.3815 0.9627
NW_003729337.1 2809 2997 1.0669 0.9781
NW_003729338.1 2772 2399 0.8654 0.8971
NW_003729339.1 2729 2697 0.9883 0.9455
NW_003729340.1 2708 2100 0.7755 0.6964
NW_003729341.1 2700 1800 0.6667 0.9027
NW_003729342.1 2641 2400 0.9087 0.9511
NW_003729343.1 2494 2703 1.0838 0.9029
NW_003729344.1 2361 2700 1.1436 0.8886
NW_003729345.1 2327 3001 1.2896 1.0391
NW_003729346.1 2250 1500 0.6667 0.6713
NW_003729347.1 2145 1800 0.8392 0.9818
NW_003729348.1 2046 2100 1.0264 0.7911
NW_003729349.1 1999 1500 0.7504 0.8041
NW_003729350.1 1819 1500 0.8246 0.671
NW_003729351.1 1790 1500 0.838 0.5568
NW_003729352.1 1685 1800 1.0682 1.0276
NW_003729353.1 1573 2400 1.5257 1.507
NW_003729354.1 1115 1500 1.3453 0.7717
NC_002008.4 16727 16801 1.0044 1.0359

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 17:21:59
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