Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/1X_hi_error_med_variance/alignment/1X_hi_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/1X_hi_error_med_variance/1X_hi_error_med_variance_R1.fa results/1X_hi_error_med_variance/1X_hi_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 17:33:42 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/1X_hi_error_med_variance/alignment/1X_hi_error_med_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 16,073,088
Mapped reads 16,072,930 / 100%
Unmapped reads 158 / 0%
Mapped paired reads 16,072,930 / 100%
Mapped reads, first in pair 8,036,458 / 50%
Mapped reads, second in pair 8,036,472 / 50%
Mapped reads, both in pair 16,072,840 / 100%
Mapped reads, singletons 90 / 0%
Secondary alignments 0
Supplementary alignments 546 / 0%
Read min/max/mean length 30 / 150 / 150
Duplicated reads (estimated) 55,128 / 0.34%
Duplication rate 0.34%
Clipped reads 1,427,897 / 8.88%

ACGT Content

Number/percentage of A's 702,970,225 / 29.32%
Number/percentage of C's 506,116,647 / 21.11%
Number/percentage of T's 692,819,554 / 28.89%
Number/percentage of G's 495,878,056 / 20.68%
Number/percentage of N's 3,803 / 0%
GC Percentage 41.79%

Coverage

Mean 0.9952
Standard Deviation 1.018

Mapping Quality

Mean Mapping Quality 30.31

Insert size

Mean 542.53
Standard Deviation 84,030.66
P25/Median/P75 315 / 349 / 383

Mismatches and indels

General error rate 5.51%
Mismatches 130,744,881
Insertions 1,105,709
Mapped reads with at least one insertion 6.66%
Deletions 1,109,705
Mapped reads with at least one deletion 6.68%
Homopolymer indels 27.57%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 122166753 0.9958 1.0152
NC_006584.3 85426708 85276611 0.9982 1.0173
NC_006585.3 91889043 91518309 0.996 1.0145
NC_006586.3 88276631 87903297 0.9958 1.0149
NC_006587.3 88915250 88509232 0.9954 1.0157
NC_006588.3 77573801 77221130 0.9955 1.0168
NC_006589.3 80974532 80629652 0.9957 1.0167
NC_006590.3 74330416 74048164 0.9962 1.0151
NC_006591.3 61074082 60903504 0.9972 1.0176
NC_006592.3 69331447 69014512 0.9954 1.0149
NC_006593.3 74389097 74075761 0.9958 1.0154
NC_006594.3 72498081 72142143 0.9951 1.016
NC_006595.3 63241923 62936034 0.9952 1.0159
NC_006596.3 60966679 60695275 0.9955 1.0142
NC_006597.3 64190966 63872285 0.995 1.0147
NC_006598.3 59632846 59424520 0.9965 1.0147
NC_006599.3 64289059 64013019 0.9957 1.0161
NC_006600.3 55844845 55601173 0.9956 1.0168
NC_006601.3 53741614 53485327 0.9952 1.0168
NC_006602.3 58134056 57854431 0.9952 1.0155
NC_006603.3 50858623 50632492 0.9956 1.0163
NC_006604.3 61439934 61123837 0.9949 1.0131
NC_006605.3 52294480 52045928 0.9952 1.0158
NC_006606.3 47698779 47504568 0.9959 1.0171
NC_006607.3 51628933 51361844 0.9948 1.0157
NC_006608.3 38964690 38808333 0.996 1.0168
NC_006609.3 45876710 45663327 0.9953 1.0149
NC_006610.3 41182112 40970941 0.9949 1.0143
NC_006611.3 41845238 41629546 0.9948 1.0119
NC_006612.3 40214260 40015487 0.9951 1.0133
NC_006613.3 39895921 39716693 0.9955 1.0147
NC_006614.3 38810281 38611591 0.9949 1.0084
NC_006615.3 31377067 31222760 0.9951 1.0118
NC_006616.3 42124431 41915880 0.995 1.0158
NC_006617.3 26524999 26382545 0.9946 1.0139
NC_006618.3 30810995 30655745 0.995 1.0133
NC_006619.3 30902991 30750252 0.9951 1.0164
NC_006620.3 23914537 23808996 0.9956 1.0137
NC_006621.3 123869142 123323349 0.9956 1.0166
NW_003726127.1 2660953 2657107 0.9986 1.0318
NW_003726128.1 1881673 1882148 1.0003 1.0713
NW_003726129.1 1415205 1412797 0.9983 1.0653
NW_003726130.1 1067467 1066134 0.9988 1.0914
NW_003726131.1 866315 863472 0.9967 1.0128
NW_003726132.1 881102 874438 0.9924 1.0437
NW_003726133.1 822601 820799 0.9978 1.0441
NW_003726134.1 741967 738408 0.9952 1.0171
NW_003726135.1 745551 743998 0.9979 1.1183
NW_003726136.1 602611 605764 1.0052 1.018
NW_003726137.1 573630 566592 0.9877 1.0126
NW_003726138.1 666183 651986 0.9787 1.1167
NW_003726139.1 557017 560519 1.0063 1.0689
NW_003726140.1 510604 517516 1.0135 1.0421
NW_003726141.1 497093 492122 0.99 1.0389
NW_003726142.1 492630 483082 0.9806 1.0304
NW_003726143.1 577062 573464 0.9938 1.1376
NW_003726144.1 561270 557970 0.9941 1.1215
NW_003726145.1 407330 404319 0.9926 1.0091
NW_003726146.1 405216 408385 1.0078 1.039
NW_003726147.1 508668 506071 0.9949 1.1433
NW_003726148.1 540093 536300 0.993 1.2056
NW_003726149.1 448434 453055 1.0103 1.1716
NW_003726150.1 377800 378885 1.0029 1.0631
NW_003726151.1 384880 381883 0.9922 1.0489
NW_003726152.1 367143 369751 1.0071 1.0367
NW_003726153.1 399987 396018 0.9901 1.0782
NW_003726154.1 376204 374470 0.9954 1.0451
NW_003726155.1 416178 405380 0.9741 1.1173
NW_003726156.1 365470 367775 1.0063 1.1043
NW_003726157.1 322752 327544 1.0148 1.026
NW_003726158.1 320591 323933 1.0104 1.0352
NW_003726159.1 310270 309016 0.996 1.0273
NW_003726160.1 433650 436470 1.0065 1.2254
NW_003726161.1 273228 276009 1.0102 1.0183
NW_003726162.1 281659 284829 1.0113 1.0402
NW_003726163.1 320442 329656 1.0288 1.1368
NW_003726164.1 265648 261369 0.9839 0.9949
NW_003726165.1 241365 253639 1.0509 1.0888
NW_003726166.1 234529 233068 0.9938 0.995
NW_003726167.1 252720 251871 0.9966 1.0971
NW_003726168.1 254975 257633 1.0104 1.0793
NW_003726169.1 226053 226244 1.0008 1.0303
NW_003726170.1 223744 228186 1.0199 1.0348
NW_003726171.1 227140 226987 0.9993 1.0325
NW_003726172.1 219672 217170 0.9886 1.0078
NW_003726173.1 214597 213832 0.9964 1.0166
NW_003726174.1 386314 381062 0.9864 1.3967
NW_003726175.1 204342 209945 1.0274 1.032
NW_003726176.1 201724 208942 1.0358 1.0386
NW_003726177.1 216332 217986 1.0076 1.0835
NW_003726178.1 200877 202424 1.0077 0.9993
NW_003726179.1 310654 307628 0.9903 1.252
NW_003726180.1 200932 198908 0.9899 1.0324
NW_003726181.1 201410 203202 1.0089 1.0264
NW_003726182.1 292533 279196 0.9544 1.1794
NW_003726183.1 192561 191291 0.9934 0.9949
NW_003726184.1 210134 215784 1.0269 1.0931
NW_003726185.1 197844 198278 1.0022 1.0727
NW_003726186.1 196813 201413 1.0234 1.0996
NW_003726187.1 180359 181983 1.009 1.0482
NW_003726188.1 210247 200735 0.9548 1.0659
NW_003726189.1 177735 185669 1.0446 1.0549
NW_003726190.1 172100 174189 1.0121 1.0297
NW_003726191.1 166866 165666 0.9928 0.9856
NW_003726192.1 164926 169253 1.0262 0.998
NW_003726193.1 157598 160490 1.0184 1.1088
NW_003726194.1 143980 143402 0.996 1.0302
NW_003726195.1 141074 139716 0.9904 1.035
NW_003726196.1 139526 137076 0.9824 0.9769
NW_003726197.1 142260 138838 0.9759 1.0425
NW_003726198.1 138160 139460 1.0094 0.9938
NW_003726199.1 142296 141831 0.9967 1.0319
NW_003726200.1 133119 132971 0.9989 1.0069
NW_003726201.1 129748 129125 0.9952 1.0772
NW_003726202.1 125962 134856 1.0706 1.0618
NW_003726203.1 127429 127177 0.998 1.033
NW_003726204.1 128261 125955 0.982 1.0086
NW_003726205.1 131872 134019 1.0163 1.0701
NW_003726206.1 133432 132676 0.9943 1.1198
NW_003726207.1 119670 121530 1.0155 1.0101
NW_003726208.1 144750 143320 0.9901 1.1301
NW_003726209.1 120779 120982 1.0017 1.0293
NW_003726210.1 115952 112442 0.9697 0.9936
NW_003726211.1 118237 111347 0.9417 1.0028
NW_003726212.1 111908 110314 0.9858 1.0169
NW_003726213.1 117332 118917 1.0135 1.0419
NW_003726214.1 111759 111334 0.9962 1.0309
NW_003726215.1 108801 109907 1.0102 1.0443
NW_003726216.1 112014 116265 1.038 1.0728
NW_003726217.1 106428 107990 1.0147 1.0413
NW_003726218.1 104912 109612 1.0448 1.0559
NW_003726219.1 104646 102584 0.9803 1.0007
NW_003726220.1 103248 100991 0.9781 1.0759
NW_003726221.1 129482 125329 0.9679 1.1413
NW_003726222.1 118473 118179 0.9975 1.1178
NW_003726223.1 99993 102382 1.0239 1.0343
NW_003726224.1 109585 107683 0.9826 1.0632
NW_003726225.1 124049 117929 0.9507 1.1284
NW_003726226.1 99658 95822 0.9615 1.0496
NW_003726227.1 101741 101226 0.9949 1.0483
NW_003726228.1 97365 101030 1.0376 1.0758
NW_003726229.1 94395 93221 0.9876 1.0021
NW_003726230.1 102992 94235 0.915 0.9976
NW_003726231.1 95509 92061 0.9639 1.0313
NW_003726232.1 92047 90790 0.9863 0.9835
NW_003726233.1 87753 93705 1.0678 1.0407
NW_003726234.1 96536 97275 1.0077 1.1094
NW_003726235.1 86544 88074 1.0177 1.0215
NW_003726236.1 85476 84832 0.9925 0.9795
NW_003726237.1 110512 112287 1.0161 1.202
NW_003726238.1 83291 83020 0.9967 1.0693
NW_003726239.1 82459 83756 1.0157 1.0547
NW_003726240.1 81605 85628 1.0493 1.0648
NW_003726241.1 82380 83506 1.0137 0.974
NW_003726242.1 102198 97211 0.9512 1.1515
NW_003726243.1 82108 81124 0.988 1.027
NW_003726244.1 87041 83495 0.9593 1.0727
NW_003726245.1 79722 81115 1.0175 1.0732
NW_003726246.1 230124 223668 0.9719 1.7091
NW_003726247.1 78357 77817 0.9931 1.0557
NW_003726248.1 256406 247812 0.9665 1.8143
NW_003726249.1 78050 74944 0.9602 0.9799
NW_003726250.1 81930 79057 0.9649 1.0226
NW_003726251.1 77100 76493 0.9921 1.0596
NW_003726252.1 77130 77637 1.0066 1.0762
NW_003726253.1 79078 82402 1.042 1.0553
NW_003726254.1 90550 90688 1.0015 1.1564
NW_003726255.1 82767 80482 0.9724 1.0425
NW_003726256.1 89070 77934 0.875 1.0006
NW_003726257.1 97802 97685 0.9988 1.1324
NW_003726258.1 79712 79363 0.9956 1.038
NW_003726259.1 79581 79897 1.004 1.1055
NW_003726260.1 73720 74087 1.005 1.0567
NW_003726261.1 97799 98314 1.0053 1.2207
NW_003726262.1 73171 70756 0.967 0.9738
NW_003726263.1 104732 97116 0.9273 1.1716
NW_003726264.1 78935 75549 0.9571 1.0922
NW_003726265.1 72992 74981 1.0272 1.0446
NW_003726266.1 68721 70167 1.021 0.9817
NW_003726267.1 73611 67082 0.9113 1.0143
NW_003726268.1 68272 68023 0.9964 1.0292
NW_003726269.1 79297 78883 0.9948 1.1298
NW_003726270.1 84443 87048 1.0308 1.1652
NW_003726271.1 80679 74852 0.9278 1.0592
NW_003726272.1 68834 68023 0.9882 1.0118
NW_003726273.1 67496 66895 0.9911 1.0176
NW_003726274.1 66523 69341 1.0424 1.0345
NW_003726275.1 67057 66909 0.9978 0.9778
NW_003726276.1 66195 67208 1.0153 1.0137
NW_003726277.1 87584 76149 0.8694 1.14
NW_003726278.1 84679 76201 0.8999 1.0623
NW_003726279.1 65840 63285 0.9612 0.9116
NW_003726280.1 65696 64489 0.9816 1.0226
NW_003726281.1 66021 66379 1.0054 1.0279
NW_003726282.1 67300 68833 1.0228 1.1018
NW_003726283.1 88153 78354 0.8888 1.1828
NW_003726284.1 92437 82255 0.8898 1.1488
NW_003726285.1 70351 71242 1.0127 1.0916
NW_003726286.1 64646 65838 1.0184 1.021
NW_003726287.1 69126 68411 0.9897 1.0496
NW_003726288.1 227674 195987 0.8608 1.7149
NW_003726289.1 64123 65000 1.0137 1.0764
NW_003726290.1 61944 60059 0.9696 1.0135
NW_003726291.1 62414 61138 0.9796 1.0157
NW_003726292.1 61779 59402 0.9615 0.9812
NW_003726293.1 90840 84761 0.9331 1.1706
NW_003726294.1 61194 61623 1.007 1.0186
NW_003726295.1 63245 65687 1.0386 1.0225
NW_003726296.1 60975 60611 0.994 1.0063
NW_003726297.1 88336 87733 0.9932 1.2189
NW_003726298.1 62896 62183 0.9887 0.9753
NW_003726299.1 60346 60151 0.9968 1.0314
NW_003726300.1 70666 66422 0.9399 1.0473
NW_003726301.1 71007 72589 1.0223 1.1907
NW_003726302.1 59879 62076 1.0367 1.0514
NW_003726303.1 59817 63873 1.0678 1.0887
NW_003726304.1 66981 61297 0.9151 0.9996
NW_003726305.1 62805 62802 1 1.0544
NW_003726306.1 68857 68108 0.9891 1.1146
NW_003726307.1 58149 60657 1.0431 0.9887
NW_003726308.1 84024 79922 0.9512 1.1858
NW_003726309.1 58658 60884 1.0379 1.0951
NW_003726310.1 65402 67646 1.0343 1.1038
NW_003726311.1 56534 52211 0.9235 0.9759
NW_003726312.1 59023 58816 0.9965 1.0783
NW_003726313.1 89903 73241 0.8147 1.1569
NW_003726314.1 54477 66972 1.2294 1.1349
NW_003726315.1 54307 54734 1.0079 1.0536
NW_003726316.1 69310 72792 1.0502 1.25
NW_003726317.1 57210 58591 1.0241 1.0222
NW_003726318.1 57907 53458 0.9232 1.0518
NW_003726319.1 53093 56359 1.0615 1.0756
NW_003726320.1 67358 58092 0.8624 1.079
NW_003726321.1 54660 56752 1.0383 1.0874
NW_003726322.1 52548 53117 1.0108 1.0177
NW_003726323.1 52637 49891 0.9478 1.0051
NW_003726324.1 51964 53485 1.0293 0.9724
NW_003726325.1 51648 57289 1.1092 1.1303
NW_003726326.1 51582 51358 0.9957 0.9896
NW_003726327.1 52288 55046 1.0527 1.1288
NW_003726328.1 50462 48138 0.9539 0.9871
NW_003726329.1 50869 51653 1.0154 1.1008
NW_003726330.1 53506 56685 1.0594 1.061
NW_003726331.1 50005 51959 1.0391 1.0176
NW_003726332.1 84691 70518 0.8327 1.1831
NW_003726333.1 63256 61202 0.9675 1.1655
NW_003726334.1 59752 58936 0.9863 1.1463
NW_003726335.1 68739 63362 0.9218 1.1601
NW_003726336.1 49027 47300 0.9648 0.9704
NW_003726337.1 49032 48762 0.9945 1.0852
NW_003726338.1 57792 55050 0.9526 1.0896
NW_003726339.1 74646 69819 0.9353 1.2469
NW_003726340.1 48411 47837 0.9881 1.0322
NW_003726341.1 48200 42129 0.874 0.9203
NW_003726342.1 75626 62087 0.821 1.093
NW_003726343.1 48436 48547 1.0023 1.0563
NW_003726344.1 47485 48099 1.0129 1.0345
NW_003726345.1 52731 51366 0.9741 1.077
NW_003726346.1 52367 51622 0.9858 1.0437
NW_003726347.1 46689 47765 1.023 1.0643
NW_003726348.1 53681 53203 0.9911 1.0944
NW_003726349.1 73441 63555 0.8654 1.1663
NW_003726350.1 57620 58385 1.0133 1.1149
NW_003726351.1 70154 64503 0.9194 1.1725
NW_003726352.1 67100 61610 0.9182 1.162
NW_003726353.1 48085 47728 0.9926 1.0974
NW_003726354.1 63970 60334 0.9432 1.1321
NW_003726355.1 45242 43627 0.9643 0.9845
NW_003726356.1 58859 45679 0.7761 1.0488
NW_003726357.1 45065 51089 1.1337 1.1242
NW_003726358.1 46098 46277 1.0039 0.984
NW_003726359.1 70370 59638 0.8475 1.2831
NW_003726360.1 46044 45626 0.9909 1.0913
NW_003726361.1 45518 45410 0.9976 1.0434
NW_003726362.1 47960 52774 1.1004 1.0755
NW_003726363.1 44571 45026 1.0102 1.0306
NW_003726364.1 84617 76142 0.8998 1.2902
NW_003726365.1 51679 49831 0.9642 1.1047
NW_003726366.1 48264 43865 0.9089 1.0292
NW_003726367.1 50939 50265 0.9868 1.0674
NW_003726368.1 72756 57329 0.788 1.1779
NW_003726369.1 44216 42788 0.9677 0.9944
NW_003726370.1 43704 43359 0.9921 0.93
NW_003726371.1 55991 52838 0.9437 1.1285
NW_003726372.1 54329 47099 0.8669 1.0966
NW_003726373.1 44549 44695 1.0033 1.0406
NW_003726374.1 44306 49903 1.1263 1.0929
NW_003726375.1 60428 55257 0.9144 1.0991
NW_003726376.1 42803 43720 1.0214 1.0804
NW_003726377.1 90666 84899 0.9364 1.4609
NW_003726378.1 42461 44185 1.0406 1.0218
NW_003726379.1 46059 45636 0.9908 1.0342
NW_003726380.1 58391 56973 0.9757 1.1634
NW_003726381.1 69503 55910 0.8044 1.0752
NW_003726382.1 41842 44471 1.0628 1.0614
NW_003726383.1 43189 46869 1.0852 1.1045
NW_003726384.1 42168 43283 1.0264 0.9946
NW_003726385.1 41454 42718 1.0305 1.0048
NW_003726386.1 43681 45652 1.0451 1.0416
NW_003726387.1 57311 57582 1.0047 1.2093
NW_003726388.1 68304 53966 0.7901 1.1056
NW_003726389.1 57240 59278 1.0356 1.3248
NW_003726390.1 42861 47174 1.1006 1.1366
NW_003726391.1 43424 41578 0.9575 1.0385
NW_003726392.1 40931 41234 1.0074 0.9718
NW_003726393.1 41221 41172 0.9988 1.0194
NW_003726394.1 41006 43655 1.0646 0.9767
NW_003726395.1 40763 44395 1.0891 1.0249
NW_003726396.1 46509 45426 0.9767 1.0478
NW_003726397.1 42743 42659 0.998 1.0343
NW_003726398.1 40517 39621 0.9779 0.9727
NW_003726399.1 40818 40458 0.9912 1.0041
NW_003726400.1 45697 46157 1.0101 1.0914
NW_003726401.1 46980 42391 0.9023 1.06
NW_003726402.1 42806 47373 1.1067 1.1739
NW_003726403.1 44573 42002 0.9423 1.0443
NW_003726404.1 39716 39128 0.9852 1.0846
NW_003726405.1 39345 39122 0.9943 1.0847
NW_003726406.1 46145 44374 0.9616 1.0612
NW_003726407.1 47441 48294 1.018 1.1824
NW_003726408.1 39138 40639 1.0384 0.9782
NW_003726409.1 40677 42654 1.0486 1.0936
NW_003726410.1 64983 58224 0.896 1.2259
NW_003726411.1 51094 51005 0.9983 1.2154
NW_003726412.1 38580 38791 1.0055 1.0682
NW_003726413.1 40054 37598 0.9387 0.9704
NW_003726414.1 39199 37929 0.9676 1.1092
NW_003726415.1 38084 39067 1.0258 1.0868
NW_003726416.1 41432 40861 0.9862 1.111
NW_003726417.1 45027 48336 1.0735 1.2139
NW_003726418.1 37707 41802 1.1086 1.0536
NW_003726419.1 59547 52889 0.8882 1.1336
NW_003726420.1 58434 51779 0.8861 1.2377
NW_003726421.1 37389 36159 0.9671 0.9385
NW_003726422.1 52308 47142 0.9012 1.09
NW_003726423.1 63560 54902 0.8638 1.2351
NW_003726424.1 69036 64471 0.9339 1.3308
NW_003726425.1 44261 41166 0.9301 1.0897
NW_003726426.1 50023 44780 0.8952 1.0501
NW_003726427.1 36777 37040 1.0072 1.0186
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NW_003729174.1 4600 3582 0.7787 0.7186
NW_003729175.1 4594 4454 0.9695 1.3182
NW_003729176.1 4588 4441 0.968 0.9685
NW_003729177.1 4580 3841 0.8386 0.968
NW_003729178.1 4577 2989 0.653 0.7318
NW_003729179.1 4577 4013 0.8768 0.8175
NW_003729180.1 4577 2696 0.589 0.8683
NW_003729181.1 4575 4712 1.0299 0.9613
NW_003729182.1 4574 4179 0.9136 0.9301
NW_003729183.1 4572 5334 1.1667 1.1478
NW_003729184.1 4572 4799 1.0497 1.0491
NW_003729185.1 4562 3992 0.8751 0.8465
NW_003729186.1 4555 3839 0.8428 0.7698
NW_003729187.1 4554 4137 0.9084 1.2148
NW_003729188.1 4552 4171 0.9163 1.2518
NW_003729189.1 4550 4162 0.9147 0.8985
NW_003729190.1 4543 5030 1.1072 1.1395
NW_003729191.1 4541 4468 0.9839 1.0711
NW_003729192.1 4539 4788 1.0549 1.0083
NW_003729193.1 4527 3852 0.8509 0.9767
NW_003729194.1 4519 4753 1.0518 0.9934
NW_003729195.1 4507 4501 0.9987 1.0295
NW_003729196.1 4501 3705 0.8232 1.137
NW_003729197.1 4485 5922 1.3204 1.027
NW_003729198.1 4480 4334 0.9674 0.9813
NW_003729199.1 4476 4146 0.9263 0.8778
NW_003729200.1 4469 4741 1.0609 1.0433
NW_003729201.1 4463 6069 1.3598 1.2984
NW_003729202.1 4460 4149 0.9303 1.1157
NW_003729203.1 4454 2981 0.6693 0.9808
NW_003729204.1 4453 5081 1.141 0.8541
NW_003729205.1 4447 4425 0.9951 1.2886
NW_003729206.1 4443 4767 1.0729 1.1598
NW_003729207.1 4439 4463 1.0054 0.8605
NW_003729208.1 4437 3895 0.8778 1.1151
NW_003729209.1 4430 2688 0.6068 0.7337
NW_003729210.1 4429 4732 1.0684 1.1375
NW_003729211.1 4428 5044 1.1391 1.1992
NW_003729212.1 4420 3549 0.8029 1.044
NW_003729213.1 4418 4770 1.0797 1.0714
NW_003729214.1 4418 4156 0.9407 0.9227
NW_003729215.1 4408 4773 1.0828 1.1219
NW_003729216.1 4404 3559 0.8081 0.7964
NW_003729217.1 4404 3815 0.8663 0.9184
NW_003729218.1 4403 4498 1.0216 0.8252
NW_003729219.1 4399 2664 0.6056 0.7798
NW_003729220.1 4393 5194 1.1823 1.3998
NW_003729221.1 4389 4459 1.0159 1.0351
NW_003729222.1 4389 2987 0.6806 0.8014
NW_003729223.1 4388 2671 0.6087 0.7532
NW_003729224.1 4378 5179 1.183 1.4794
NW_003729225.1 4368 4781 1.0946 1.0702
NW_003729226.1 4359 4206 0.9649 1.0242
NW_003729227.1 4356 2979 0.6839 1.0954
NW_003729228.1 4353 3874 0.89 0.8616
NW_003729229.1 4329 3119 0.7205 0.7346
NW_003729230.1 4311 5032 1.1672 1.7019
NW_003729231.1 4302 2034 0.4728 0.7623
NW_003729232.1 4300 4270 0.993 1.3445
NW_003729233.1 4285 3257 0.7601 0.7501
NW_003729234.1 4283 3848 0.8984 1.0974
NW_003729235.1 4282 3567 0.833 0.8063
NW_003729236.1 4281 4491 1.0491 0.7903
NW_003729237.1 4279 2701 0.6312 0.9315
NW_003729238.1 4277 4178 0.9769 0.9164
NW_003729239.1 4276 3228 0.7549 0.9472
NW_003729240.1 4276 2078 0.486 0.5935
NW_003729241.1 4252 3899 0.917 0.8634
NW_003729242.1 4248 4191 0.9866 0.825
NW_003729243.1 4239 4457 1.0514 0.952
NW_003729244.1 4238 4729 1.1159 1.1817
NW_003729245.1 4234 4146 0.9792 0.925
NW_003729246.1 4233 2684 0.6341 0.7525
NW_003729247.1 4231 4468 1.056 1.0185
NW_003729248.1 4225 4697 1.1117 0.9622
NW_003729249.1 4201 7068 1.6825 1.5659
NW_003729250.1 4198 3420 0.8147 0.9554
NW_003729251.1 4193 4443 1.0596 1.1879
NW_003729252.1 4186 4128 0.9861 0.9046
NW_003729253.1 4183 3364 0.8042 0.8791
NW_003729254.1 4177 3518 0.8422 0.9579
NW_003729255.1 4172 3276 0.7852 0.7657
NW_003729256.1 4163 4787 1.1499 1.0575
NW_003729257.1 4156 4142 0.9966 1.1632
NW_003729258.1 4141 2676 0.6462 0.9469
NW_003729259.1 4130 4173 1.0104 1.0522
NW_003729260.1 4130 2639 0.639 0.8642
NW_003729261.1 4126 4484 1.0868 1.2079
NW_003729262.1 4123 3299 0.8001 0.9836
NW_003729263.1 4121 4599 1.116 1.2893
NW_003729264.1 4117 4174 1.0138 0.8285
NW_003729265.1 4112 4123 1.0027 0.9065
NW_003729266.1 4097 2371 0.5787 0.8356
NW_003729267.1 4096 3426 0.8364 0.8139
NW_003729268.1 4070 6482 1.5926 1.3233
NW_003729269.1 4064 4477 1.1016 1.0841
NW_003729270.1 4061 3897 0.9596 1.0111
NW_003729271.1 4060 3840 0.9458 1.012
NW_003729272.1 4025 4106 1.0201 1.0827
NW_003729273.1 4025 4170 1.036 1.1675
NW_003729274.1 4011 4196 1.0461 1.1705
NW_003729275.1 4001 4032 1.0077 0.9351
NW_003729276.1 3976 3863 0.9716 1.0326
NW_003729277.1 3948 4032 1.0213 0.9798
NW_003729278.1 3941 3812 0.9673 1.4244
NW_003729279.1 3928 3409 0.8679 0.9577
NW_003729280.1 3925 3863 0.9842 1.0725
NW_003729281.1 3919 2682 0.6844 0.9408
NW_003729282.1 3849 2384 0.6194 0.7014
NW_003729283.1 3848 2346 0.6097 0.7741
NW_003729284.1 3847 3245 0.8435 0.9478
NW_003729285.1 3817 4464 1.1695 1.2583
NW_003729286.1 3780 3252 0.8603 1.0536
NW_003729287.1 3780 4176 1.1048 0.9623
NW_003729288.1 3777 3583 0.9486 1.2242
NW_003729289.1 3761 3249 0.8639 0.9631
NW_003729290.1 3750 3877 1.0339 1.2393
NW_003729291.1 3733 3576 0.9579 1.0091
NW_003729292.1 3719 3694 0.9933 0.8471
NW_003729293.1 3718 4175 1.1229 1.1182
NW_003729294.1 3706 3543 0.956 0.9387
NW_003729295.1 3700 3938 1.0643 1.037
NW_003729296.1 3695 2661 0.7202 0.9509
NW_003729297.1 3652 4022 1.1013 1.1704
NW_003729298.1 3649 4715 1.2921 1.6263
NW_003729299.1 3629 2342 0.6454 0.6446
NW_003729300.1 3622 3569 0.9854 0.8785
NW_003729301.1 3616 3981 1.1009 1.0291
NW_003729302.1 3614 3565 0.9864 1.037
NW_003729303.1 3595 3870 1.0765 0.9329
NW_003729304.1 3589 6039 1.6826 1.3358
NW_003729305.1 3585 3734 1.0416 1.1152
NW_003729306.1 3580 3590 1.0028 0.8367
NW_003729307.1 3576 3685 1.0305 0.9596
NW_003729308.1 3564 2656 0.7452 0.8212
NW_003729309.1 3524 2678 0.7599 0.9308
NW_003729310.1 3506 3262 0.9304 0.9338
NW_003729311.1 3484 2984 0.8565 0.9477
NW_003729312.1 3480 1460 0.4195 0.8414
NW_003729313.1 3479 2926 0.841 0.988
NW_003729314.1 3440 2990 0.8692 0.8127
NW_003729315.1 3431 3582 1.044 1.1644
NW_003729316.1 3430 3856 1.1242 1.088
NW_003729317.1 3407 2681 0.7869 0.9865
NW_003729318.1 3398 3825 1.1257 1.1549
NW_003729319.1 3393 3230 0.952 1.0238
NW_003729320.1 3388 3563 1.0517 1.0993
NW_003729321.1 3369 2696 0.8002 0.9828
NW_003729322.1 3338 2650 0.7939 1.1505
NW_003729323.1 3331 2966 0.8904 1.2008
NW_003729324.1 3271 2972 0.9086 1.177
NW_003729325.1 3257 3257 1 1.4075
NW_003729326.1 3257 3291 1.0104 1.0586
NW_003729327.1 3231 1800 0.5571 0.808
NW_003729328.1 3135 2681 0.8552 1.0805
NW_003729329.1 3134 2675 0.8535 0.8629
NW_003729330.1 3059 2993 0.9784 1.0135
NW_003729331.1 3011 3296 1.0947 0.9413
NW_003729332.1 2997 2080 0.694 0.6833
NW_003729333.1 2955 3852 1.3036 1.0463
NW_003729334.1 2933 1784 0.6083 0.5755
NW_003729335.1 2850 2388 0.8379 0.9117
NW_003729336.1 2823 1795 0.6358 0.6437
NW_003729337.1 2809 1456 0.5183 0.9051
NW_003729338.1 2772 1139 0.4109 0.7675
NW_003729339.1 2729 2698 0.9886 1.2099
NW_003729340.1 2708 3307 1.2212 1.1768
NW_003729341.1 2700 2080 0.7704 1.0488
NW_003729342.1 2641 2676 1.0133 1.24
NW_003729343.1 2494 2638 1.0577 1.0842
NW_003729344.1 2361 1799 0.762 0.8933
NW_003729345.1 2327 2401 1.0318 0.9533
NW_003729346.1 2250 1800 0.8 1.005
NW_003729347.1 2145 599 0.2793 0.4484
NW_003729348.1 2046 2390 1.1681 1.1922
NW_003729349.1 1999 2398 1.1996 0.9809
NW_003729350.1 1819 1768 0.972 0.8381
NW_003729351.1 1790 2096 1.1709 1.0014
NW_003729352.1 1685 1779 1.0558 1.0593
NW_003729353.1 1573 1501 0.9542 0.9685
NW_003729354.1 1115 1196 1.0726 0.8634
NC_002008.4 16727 16675 0.9969 0.9949

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 17:33:42
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