Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/1X_hi_error_no_variance/alignment/1X_hi_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_hi_error_no_variance/1X_hi_error_no_variance_R1.fa results/1X_hi_error_no_variance/1X_hi_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 17:32:15 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/1X_hi_error_no_variance/alignment/1X_hi_error_no_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 16,073,088
Mapped reads 16,073,035 / 100%
Unmapped reads 53 / 0%
Mapped paired reads 16,073,035 / 100%
Mapped reads, first in pair 8,036,517 / 50%
Mapped reads, second in pair 8,036,518 / 50%
Mapped reads, both in pair 16,073,006 / 100%
Mapped reads, singletons 29 / 0%
Secondary alignments 0
Supplementary alignments 294 / 0%
Read min/max/mean length 30 / 150 / 150
Duplicated reads (estimated) 54,691 / 0.34%
Duplication rate 0.34%
Clipped reads 1,031,723 / 6.42%

ACGT Content

Number/percentage of A's 705,425,916 / 29.35%
Number/percentage of C's 506,563,643 / 21.08%
Number/percentage of T's 695,170,285 / 28.92%
Number/percentage of G's 496,254,098 / 20.65%
Number/percentage of N's 3,956 / 0%
GC Percentage 41.72%

Coverage

Mean 0.9969
Standard Deviation 1.0192

Mapping Quality

Mean Mapping Quality 30.64

Insert size

Mean 502.67
Standard Deviation 78,157.31
P25/Median/P75 316 / 349 / 383

Mismatches and indels

General error rate 4.9%
Mismatches 117,695,899
Insertions 13,917
Mapped reads with at least one insertion 0.09%
Deletions 11,121
Mapped reads with at least one deletion 0.07%
Homopolymer indels 25.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 122383452 0.9976 1.0166
NC_006584.3 85426708 85430902 1 1.0189
NC_006585.3 91889043 91695016 0.9979 1.0148
NC_006586.3 88276631 88061462 0.9976 1.0168
NC_006587.3 88915250 88653470 0.9971 1.0154
NC_006588.3 77573801 77364310 0.9973 1.0165
NC_006589.3 80974532 80767548 0.9974 1.016
NC_006590.3 74330416 74113738 0.9971 1.0171
NC_006591.3 61074082 61030409 0.9993 1.0202
NC_006592.3 69331447 69111209 0.9968 1.0165
NC_006593.3 74389097 74184855 0.9973 1.0158
NC_006594.3 72498081 72270690 0.9969 1.0173
NC_006595.3 63241923 63077379 0.9974 1.0163
NC_006596.3 60966679 60805418 0.9974 1.0173
NC_006597.3 64190966 63987201 0.9968 1.0172
NC_006598.3 59632846 59554314 0.9987 1.0197
NC_006599.3 64289059 64143572 0.9977 1.0162
NC_006600.3 55844845 55688490 0.9972 1.0175
NC_006601.3 53741614 53581633 0.997 1.0155
NC_006602.3 58134056 57949153 0.9968 1.0183
NC_006603.3 50858623 50708518 0.997 1.0158
NC_006604.3 61439934 61251579 0.9969 1.0132
NC_006605.3 52294480 52104923 0.9964 1.0124
NC_006606.3 47698779 47569002 0.9973 1.0156
NC_006607.3 51628933 51446648 0.9965 1.0142
NC_006608.3 38964690 38894342 0.9982 1.0187
NC_006609.3 45876710 45720936 0.9966 1.0184
NC_006610.3 41182112 41050685 0.9968 1.0173
NC_006611.3 41845238 41702955 0.9966 1.0139
NC_006612.3 40214260 40085292 0.9968 1.017
NC_006613.3 39895921 39755890 0.9965 1.0136
NC_006614.3 38810281 38677949 0.9966 1.0141
NC_006615.3 31377067 31283794 0.997 1.0157
NC_006616.3 42124431 41979777 0.9966 1.017
NC_006617.3 26524999 26438964 0.9968 1.0148
NC_006618.3 30810995 30704354 0.9965 1.0146
NC_006619.3 30902991 30798264 0.9966 1.017
NC_006620.3 23914537 23857678 0.9976 1.0195
NC_006621.3 123869142 123533020 0.9973 1.0185
NW_003726127.1 2660953 2663167 1.0008 1.0262
NW_003726128.1 1881673 1887480 1.0031 1.0687
NW_003726129.1 1415205 1420419 1.0037 1.0662
NW_003726130.1 1067467 1068600 1.0011 1.1075
NW_003726131.1 866315 862549 0.9957 1.0087
NW_003726132.1 881102 885542 1.005 1.0586
NW_003726133.1 822601 828381 1.007 1.0626
NW_003726134.1 741967 747876 1.008 1.0272
NW_003726135.1 745551 737561 0.9893 1.1128
NW_003726136.1 602611 608523 1.0098 1.0313
NW_003726137.1 573630 570617 0.9947 1.0491
NW_003726138.1 666183 659418 0.9898 1.0967
NW_003726139.1 557017 559754 1.0049 1.0673
NW_003726140.1 510604 508189 0.9953 1.0007
NW_003726141.1 497093 498497 1.0028 1.0321
NW_003726142.1 492630 487359 0.9893 1.0289
NW_003726143.1 577062 574888 0.9962 1.1476
NW_003726144.1 561270 554758 0.9884 1.1348
NW_003726145.1 407330 407270 0.9999 1.0128
NW_003726146.1 405216 412045 1.0169 1.0354
NW_003726147.1 508668 505331 0.9934 1.1354
NW_003726148.1 540093 538495 0.997 1.2167
NW_003726149.1 448434 446381 0.9954 1.0929
NW_003726150.1 377800 377568 0.9994 1.0528
NW_003726151.1 384880 383088 0.9953 1.0813
NW_003726152.1 367143 370667 1.0096 1.0377
NW_003726153.1 399987 402009 1.0051 1.074
NW_003726154.1 376204 370541 0.9849 1.0404
NW_003726155.1 416178 413153 0.9927 1.1043
NW_003726156.1 365470 364512 0.9974 1.065
NW_003726157.1 322752 331837 1.0281 1.0412
NW_003726158.1 320591 321853 1.0039 1.019
NW_003726159.1 310270 311486 1.0039 1.0351
NW_003726160.1 433650 424365 0.9786 1.1914
NW_003726161.1 273228 275958 1.01 1.0055
NW_003726162.1 281659 276772 0.9826 1.0219
NW_003726163.1 320442 320715 1.0009 1.1341
NW_003726164.1 265648 266631 1.0037 1.0163
NW_003726165.1 241365 250398 1.0374 1.0298
NW_003726166.1 234529 233422 0.9953 1.0072
NW_003726167.1 252720 262167 1.0374 1.099
NW_003726168.1 254975 255845 1.0034 1.1087
NW_003726169.1 226053 224705 0.994 0.9873
NW_003726170.1 223744 226913 1.0142 1.0599
NW_003726171.1 227140 229714 1.0113 1.0179
NW_003726172.1 219672 219672 1 1.0123
NW_003726173.1 214597 215268 1.0031 1.011
NW_003726174.1 386314 386045 0.9993 1.3726
NW_003726175.1 204342 206115 1.0087 0.9892
NW_003726176.1 201724 203791 1.0102 1.0759
NW_003726177.1 216332 214638 0.9922 1.0822
NW_003726178.1 200877 199709 0.9942 0.9943
NW_003726179.1 310654 299473 0.964 1.2307
NW_003726180.1 200932 199937 0.995 1.0215
NW_003726181.1 201410 196439 0.9753 1.0329
NW_003726182.1 292533 281162 0.9611 1.1847
NW_003726183.1 192561 194877 1.012 0.9944
NW_003726184.1 210134 206993 0.9851 1.049
NW_003726185.1 197844 206110 1.0418 1.1003
NW_003726186.1 196813 206007 1.0467 1.0814
NW_003726187.1 180359 181857 1.0083 1.0312
NW_003726188.1 210247 196474 0.9345 1.0798
NW_003726189.1 177735 183060 1.03 1.0295
NW_003726190.1 172100 177528 1.0315 1.0784
NW_003726191.1 166866 169801 1.0176 1.0289
NW_003726192.1 164926 167634 1.0164 1.0256
NW_003726193.1 157598 155300 0.9854 1.0806
NW_003726194.1 143980 143614 0.9975 1.0091
NW_003726195.1 141074 138832 0.9841 1.029
NW_003726196.1 139526 141578 1.0147 1.0131
NW_003726197.1 142260 143150 1.0063 1.0453
NW_003726198.1 138160 141767 1.0261 1.0399
NW_003726199.1 142296 146809 1.0317 1.0782
NW_003726200.1 133119 132348 0.9942 1.0375
NW_003726201.1 129748 129362 0.997 1.0168
NW_003726202.1 125962 129142 1.0252 1.0252
NW_003726203.1 127429 126535 0.993 1.0041
NW_003726204.1 128261 124292 0.9691 0.9937
NW_003726205.1 131872 131453 0.9968 1.06
NW_003726206.1 133432 137538 1.0308 1.0899
NW_003726207.1 119670 125470 1.0485 1.0715
NW_003726208.1 144750 142901 0.9872 1.1089
NW_003726209.1 120779 116323 0.9631 1.0038
NW_003726210.1 115952 114198 0.9849 1.051
NW_003726211.1 118237 108356 0.9164 0.9432
NW_003726212.1 111908 112427 1.0046 1.0213
NW_003726213.1 117332 117442 1.0009 1.0423
NW_003726214.1 111759 111544 0.9981 1.0022
NW_003726215.1 108801 114468 1.0521 1.0347
NW_003726216.1 112014 111313 0.9937 1.071
NW_003726217.1 106428 105552 0.9918 1.0215
NW_003726218.1 104912 104592 0.9969 0.9917
NW_003726219.1 104646 103417 0.9883 0.9898
NW_003726220.1 103248 99574 0.9644 1.0269
NW_003726221.1 129482 126491 0.9769 1.1417
NW_003726222.1 118473 119681 1.0102 1.1151
NW_003726223.1 99993 104287 1.0429 1.0507
NW_003726224.1 109585 111265 1.0153 1.015
NW_003726225.1 124049 112493 0.9068 1.0816
NW_003726226.1 99658 96712 0.9704 1.0437
NW_003726227.1 101741 101477 0.9974 1.0369
NW_003726228.1 97365 99097 1.0178 1.0601
NW_003726229.1 94395 93984 0.9956 1.019
NW_003726230.1 102992 101735 0.9878 1.0689
NW_003726231.1 95509 92318 0.9666 1.0799
NW_003726232.1 92047 90201 0.9799 1.0109
NW_003726233.1 87753 86086 0.981 0.9937
NW_003726234.1 96536 101361 1.05 1.0966
NW_003726235.1 86544 88038 1.0173 1.0241
NW_003726236.1 85476 85555 1.0009 0.9645
NW_003726237.1 110512 112488 1.0179 1.1954
NW_003726238.1 83291 83502 1.0025 1.0416
NW_003726239.1 82459 85469 1.0365 0.98
NW_003726240.1 81605 86665 1.062 0.9845
NW_003726241.1 82380 83276 1.0109 1.0514
NW_003726242.1 102198 99069 0.9694 1.173
NW_003726243.1 82108 80142 0.9761 1.0757
NW_003726244.1 87041 82912 0.9526 1.0298
NW_003726245.1 79722 79287 0.9945 1.0259
NW_003726246.1 230124 224599 0.976 1.7125
NW_003726247.1 78357 77558 0.9898 1.0371
NW_003726248.1 256406 252625 0.9853 1.8129
NW_003726249.1 78050 78578 1.0068 0.9739
NW_003726250.1 81930 83593 1.0203 1.1085
NW_003726251.1 77100 80378 1.0425 1.031
NW_003726252.1 77130 78052 1.012 0.9719
NW_003726253.1 79078 79625 1.0069 1.0011
NW_003726254.1 90550 85276 0.9418 1.0957
NW_003726255.1 82767 85467 1.0326 1.141
NW_003726256.1 89070 89189 1.0013 1.134
NW_003726257.1 97802 95247 0.9739 1.1453
NW_003726258.1 79712 79468 0.9969 1.0317
NW_003726259.1 79581 77470 0.9735 1.029
NW_003726260.1 73720 72602 0.9848 0.9957
NW_003726261.1 97799 94450 0.9658 1.0918
NW_003726262.1 73171 75057 1.0258 1.0038
NW_003726263.1 104732 104574 0.9985 1.2101
NW_003726264.1 78935 72169 0.9143 1.0094
NW_003726265.1 72992 71729 0.9827 1.0723
NW_003726266.1 68721 72510 1.0551 1.0488
NW_003726267.1 73611 73532 0.9989 1.0521
NW_003726268.1 68272 67635 0.9907 1.0133
NW_003726269.1 79297 77784 0.9809 1.1146
NW_003726270.1 84443 84276 0.998 1.1074
NW_003726271.1 80679 81722 1.0129 1.0908
NW_003726272.1 68834 65737 0.955 1.0224
NW_003726273.1 67496 67296 0.997 1.1272
NW_003726274.1 66523 66197 0.9951 0.9953
NW_003726275.1 67057 67320 1.0039 1.0209
NW_003726276.1 66195 65988 0.9969 1.032
NW_003726277.1 87584 81176 0.9268 1.153
NW_003726278.1 84679 81631 0.964 1.0874
NW_003726279.1 65840 65777 0.999 0.9783
NW_003726280.1 65696 67624 1.0293 0.9185
NW_003726281.1 66021 64891 0.9829 0.9999
NW_003726282.1 67300 70431 1.0465 1.0468
NW_003726283.1 88153 84050 0.9535 1.1456
NW_003726284.1 92437 86617 0.937 1.206
NW_003726285.1 70351 69417 0.9867 1.0755
NW_003726286.1 64646 67050 1.0372 1.116
NW_003726287.1 69126 68904 0.9968 1.0202
NW_003726288.1 227674 206073 0.9051 1.7614
NW_003726289.1 64123 63744 0.9941 1.0656
NW_003726290.1 61944 59895 0.9669 0.9975
NW_003726291.1 62414 64531 1.0339 1.0347
NW_003726292.1 61779 61821 1.0007 1.0525
NW_003726293.1 90840 81944 0.9021 1.1602
NW_003726294.1 61194 63383 1.0358 0.9772
NW_003726295.1 63245 61038 0.9651 0.9981
NW_003726296.1 60975 58624 0.9614 1.0377
NW_003726297.1 88336 79332 0.8981 1.1406
NW_003726298.1 62896 52386 0.8329 0.9165
NW_003726299.1 60346 56233 0.9318 1.0069
NW_003726300.1 70666 59795 0.8462 0.9614
NW_003726301.1 71007 79159 1.1148 1.1688
NW_003726302.1 59879 61643 1.0295 1.0612
NW_003726303.1 59817 63995 1.0698 1.0637
NW_003726304.1 66981 64976 0.9701 1.1035
NW_003726305.1 62805 63110 1.0049 1.0438
NW_003726306.1 68857 71020 1.0314 1.1418
NW_003726307.1 58149 61389 1.0557 1.0073
NW_003726308.1 84024 77460 0.9219 1.1546
NW_003726309.1 58658 60810 1.0367 0.9998
NW_003726310.1 65402 64553 0.987 1.1244
NW_003726311.1 56534 55354 0.9791 1.0665
NW_003726312.1 59023 61342 1.0393 1.0178
NW_003726313.1 89903 71222 0.7922 1.1699
NW_003726314.1 54477 62640 1.1498 1.1357
NW_003726315.1 54307 52036 0.9582 0.9949
NW_003726316.1 69310 64406 0.9292 1.1705
NW_003726317.1 57210 58041 1.0145 1.0893
NW_003726318.1 57907 54692 0.9445 1.0739
NW_003726319.1 53093 52099 0.9813 1.0822
NW_003726320.1 67358 58056 0.8619 1.0707
NW_003726321.1 54660 55021 1.0066 1.0755
NW_003726322.1 52548 51116 0.9727 1.0038
NW_003726323.1 52637 52513 0.9976 0.9636
NW_003726324.1 51964 54719 1.053 1.0795
NW_003726325.1 51648 58038 1.1237 1.0008
NW_003726326.1 51582 49671 0.963 0.9854
NW_003726327.1 52288 53306 1.0195 1.0392
NW_003726328.1 50462 51044 1.0115 0.9771
NW_003726329.1 50869 51689 1.0161 1.0816
NW_003726330.1 53506 51143 0.9558 0.9984
NW_003726331.1 50005 50845 1.0168 1.0135
NW_003726332.1 84691 66044 0.7798 1.1096
NW_003726333.1 63256 58974 0.9323 1.1243
NW_003726334.1 59752 57984 0.9704 1.0715
NW_003726335.1 68739 62206 0.905 1.2244
NW_003726336.1 49027 49960 1.019 0.9939
NW_003726337.1 49032 46666 0.9517 0.9868
NW_003726338.1 57792 59904 1.0365 1.2134
NW_003726339.1 74646 63121 0.8456 1.173
NW_003726340.1 48411 48477 1.0014 1.0095
NW_003726341.1 48200 45728 0.9487 0.9599
NW_003726342.1 75626 62751 0.8298 1.1594
NW_003726343.1 48436 49372 1.0193 0.9913
NW_003726344.1 47485 45710 0.9626 0.983
NW_003726345.1 52731 51496 0.9766 1.1232
NW_003726346.1 52367 53091 1.0138 1.07
NW_003726347.1 46689 45464 0.9738 0.975
NW_003726348.1 53681 50190 0.935 1.0131
NW_003726349.1 73441 67530 0.9195 1.2155
NW_003726350.1 57620 55364 0.9608 1.0629
NW_003726351.1 70154 68469 0.976 1.3475
NW_003726352.1 67100 61234 0.9126 1.1757
NW_003726353.1 48085 47580 0.9895 1.0051
NW_003726354.1 63970 64621 1.0102 1.21
NW_003726355.1 45242 44200 0.977 1.0183
NW_003726356.1 58859 54198 0.9208 1.0981
NW_003726357.1 45065 44725 0.9925 1.0433
NW_003726358.1 46098 47911 1.0393 1.0856
NW_003726359.1 70370 62708 0.8911 1.3365
NW_003726360.1 46044 45788 0.9944 1.0181
NW_003726361.1 45518 44849 0.9853 1.0442
NW_003726362.1 47960 50530 1.0536 1.187
NW_003726363.1 44571 44197 0.9916 1.0056
NW_003726364.1 84617 73820 0.8724 1.3099
NW_003726365.1 51679 53834 1.0417 1.0758
NW_003726366.1 48264 49083 1.017 1.0961
NW_003726367.1 50939 47073 0.9241 1.1608
NW_003726368.1 72756 61857 0.8502 1.2556
NW_003726369.1 44216 43698 0.9883 1.0555
NW_003726370.1 43704 43376 0.9925 1.0681
NW_003726371.1 55991 54412 0.9718 1.1799
NW_003726372.1 54329 48064 0.8847 1.1091
NW_003726373.1 44549 45692 1.0257 1.0525
NW_003726374.1 44306 42929 0.9689 1.0682
NW_003726375.1 60428 53157 0.8797 1.1695
NW_003726376.1 42803 43365 1.0131 1.0787
NW_003726377.1 90666 79779 0.8799 1.4118
NW_003726378.1 42461 42196 0.9938 0.9876
NW_003726379.1 46059 46821 1.0165 1.0909
NW_003726380.1 58391 55857 0.9566 1.1025
NW_003726381.1 69503 58583 0.8429 1.2015
NW_003726382.1 41842 41842 1 0.9565
NW_003726383.1 43189 50815 1.1766 1.1341
NW_003726384.1 42168 40625 0.9634 0.9857
NW_003726385.1 41454 39197 0.9456 0.9542
NW_003726386.1 43681 43505 0.996 1.0697
NW_003726387.1 57311 58682 1.0239 1.1966
NW_003726388.1 68304 55080 0.8064 1.094
NW_003726389.1 57240 53593 0.9363 1.2014
NW_003726390.1 42861 43991 1.0264 1.0695
NW_003726391.1 43424 44200 1.0179 1.0622
NW_003726392.1 40931 40998 1.0016 1.0138
NW_003726393.1 41221 40030 0.9711 1.0068
NW_003726394.1 41006 40903 0.9975 1.0033
NW_003726395.1 40763 44249 1.0855 1.0032
NW_003726396.1 46509 46148 0.9922 1.1171
NW_003726397.1 42743 41599 0.9732 1.0459
NW_003726398.1 40517 41547 1.0254 0.9836
NW_003726399.1 40818 40050 0.9812 0.9742
NW_003726400.1 45697 42295 0.9256 1.0256
NW_003726401.1 46980 43020 0.9157 1.0576
NW_003726402.1 42806 41226 0.9631 1.1255
NW_003726403.1 44573 41792 0.9376 1.0628
NW_003726404.1 39716 39427 0.9927 0.9866
NW_003726405.1 39345 38858 0.9876 1.0336
NW_003726406.1 46145 45622 0.9887 1.0892
NW_003726407.1 47441 42513 0.8961 1.0772
NW_003726408.1 39138 39787 1.0166 1.093
NW_003726409.1 40677 42064 1.0341 1.0357
NW_003726410.1 64983 61662 0.9489 1.3108
NW_003726411.1 51094 44846 0.8777 1.1966
NW_003726412.1 38580 43354 1.1237 1.0113
NW_003726413.1 40054 40943 1.0222 1.0804
NW_003726414.1 39199 39824 1.0159 1.0619
NW_003726415.1 38084 41558 1.0912 1.0696
NW_003726416.1 41432 42509 1.026 1.0607
NW_003726417.1 45027 39457 0.8763 0.9923
NW_003726418.1 37707 42500 1.1271 1.0465
NW_003726419.1 59547 55476 0.9316 1.2393
NW_003726420.1 58434 51209 0.8764 1.1623
NW_003726421.1 37389 35868 0.9593 0.9567
NW_003726422.1 52308 47000 0.8985 1.154
NW_003726423.1 63560 53525 0.8421 1.2329
NW_003726424.1 69036 64305 0.9315 1.3265
NW_003726425.1 44261 36174 0.8173 1.024
NW_003726426.1 50023 48125 0.9621 1.1854
NW_003726427.1 36777 34959 0.9506 0.9799
NW_003726428.1 63789 58834 0.9223 1.2911
NW_003726429.1 56472 53208 0.9422 1.2195
NW_003726430.1 36805 38004 1.0326 1.0613
NW_003726431.1 36868 40017 1.0854 1.0737
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NW_003729175.1 4594 5068 1.1032 1.0386
NW_003729176.1 4588 4469 0.9741 0.9969
NW_003729177.1 4580 3290 0.7183 0.7887
NW_003729178.1 4577 5076 1.109 1.1191
NW_003729179.1 4577 4774 1.043 1.3808
NW_003729180.1 4577 5379 1.1752 1.1758
NW_003729181.1 4575 5529 1.2085 1.0879
NW_003729182.1 4574 2086 0.4561 0.7805
NW_003729183.1 4572 3875 0.8476 0.9692
NW_003729184.1 4572 4176 0.9134 1.0242
NW_003729185.1 4562 4482 0.9825 1.1297
NW_003729186.1 4555 4140 0.9089 1.1103
NW_003729187.1 4554 5453 1.1974 1.1119
NW_003729188.1 4552 5655 1.2423 1.1156
NW_003729189.1 4550 4167 0.9158 0.8091
NW_003729190.1 4543 5684 1.2512 1.1258
NW_003729191.1 4541 4785 1.0537 1.3664
NW_003729192.1 4539 4489 0.989 0.9176
NW_003729193.1 4527 4028 0.8898 0.877
NW_003729194.1 4519 5663 1.2532 1.1288
NW_003729195.1 4507 5096 1.1307 1.0813
NW_003729196.1 4501 2935 0.6521 1.1713
NW_003729197.1 4485 4312 0.9614 1.2434
NW_003729198.1 4480 5669 1.2654 1.0205
NW_003729199.1 4476 5682 1.2694 1.187
NW_003729200.1 4469 4776 1.0687 1.265
NW_003729201.1 4463 5517 1.2362 1.1985
NW_003729202.1 4460 4480 1.0045 1.1571
NW_003729203.1 4454 4180 0.9385 1.0221
NW_003729204.1 4453 4004 0.8992 0.8006
NW_003729205.1 4447 4158 0.935 0.9642
NW_003729206.1 4443 5057 1.1382 1.124
NW_003729207.1 4439 4500 1.0137 1.0053
NW_003729208.1 4437 3293 0.7422 0.9153
NW_003729209.1 4430 4473 1.0097 0.8686
NW_003729210.1 4429 4193 0.9467 1.0157
NW_003729211.1 4428 4585 1.0355 1.0542
NW_003729212.1 4420 3576 0.809 1.0089
NW_003729213.1 4418 4779 1.0817 1.4021
NW_003729214.1 4418 3282 0.7429 0.7855
NW_003729215.1 4408 5388 1.2223 1.0631
NW_003729216.1 4404 4907 1.1142 0.869
NW_003729217.1 4404 3863 0.8772 1.1247
NW_003729218.1 4403 4500 1.022 0.8635
NW_003729219.1 4399 3540 0.8047 0.9461
NW_003729220.1 4393 3400 0.774 0.9318
NW_003729221.1 4389 3565 0.8123 0.8909
NW_003729222.1 4389 4343 0.9895 1.1106
NW_003729223.1 4388 4154 0.9467 0.9269
NW_003729224.1 4378 2969 0.6782 0.8031
NW_003729225.1 4368 3295 0.7543 0.7914
NW_003729226.1 4359 4495 1.0312 1.1443
NW_003729227.1 4356 4470 1.0262 1.2103
NW_003729228.1 4353 5684 1.3058 1.1709
NW_003729229.1 4329 3579 0.8267 0.9563
NW_003729230.1 4311 5208 1.2081 1.3344
NW_003729231.1 4302 5047 1.1732 1.0548
NW_003729232.1 4300 3296 0.7665 0.8786
NW_003729233.1 4285 3728 0.87 0.8321
NW_003729234.1 4283 3872 0.904 1.2318
NW_003729235.1 4282 3582 0.8365 1.0684
NW_003729236.1 4281 3887 0.908 1.1858
NW_003729237.1 4279 4172 0.975 1.1263
NW_003729238.1 4277 3281 0.7671 1.1324
NW_003729239.1 4276 4480 1.0477 1.0174
NW_003729240.1 4276 1492 0.3489 0.5366
NW_003729241.1 4252 3893 0.9156 0.8231
NW_003729242.1 4248 5218 1.2283 1.2093
NW_003729243.1 4239 3571 0.8424 1.062
NW_003729244.1 4238 2973 0.7015 0.976
NW_003729245.1 4234 3588 0.8474 0.9425
NW_003729246.1 4233 3123 0.7378 0.8201
NW_003729247.1 4231 3698 0.874 1.0468
NW_003729248.1 4225 5907 1.3981 1.5322
NW_003729249.1 4201 4449 1.059 1.0356
NW_003729250.1 4198 4128 0.9833 1.2073
NW_003729251.1 4193 2926 0.6978 0.6806
NW_003729252.1 4186 6275 1.499 1.4049
NW_003729253.1 4183 4785 1.1439 1.0682
NW_003729254.1 4177 3549 0.8497 0.8239
NW_003729255.1 4172 2235 0.5357 0.6204
NW_003729256.1 4163 5096 1.2241 0.98
NW_003729257.1 4156 4761 1.1456 1.0367
NW_003729258.1 4141 2983 0.7204 0.8036
NW_003729259.1 4130 4200 1.0169 0.8084
NW_003729260.1 4130 3557 0.8613 0.9179
NW_003729261.1 4126 3265 0.7913 1.0194
NW_003729262.1 4123 3597 0.8724 0.9047
NW_003729263.1 4121 2083 0.5055 0.8322
NW_003729264.1 4117 3900 0.9473 1.1169
NW_003729265.1 4112 3582 0.8711 0.8936
NW_003729266.1 4097 4137 1.0098 0.8287
NW_003729267.1 4096 4140 1.0107 1.0516
NW_003729268.1 4070 5391 1.3246 1.5724
NW_003729269.1 4064 2689 0.6617 0.9014
NW_003729270.1 4061 3281 0.8079 0.9321
NW_003729271.1 4060 5611 1.382 1.0352
NW_003729272.1 4025 2674 0.6643 0.6956
NW_003729273.1 4025 2983 0.7411 0.8994
NW_003729274.1 4011 3538 0.8821 1.0251
NW_003729275.1 4001 3554 0.8883 0.9108
NW_003729276.1 3976 3263 0.8207 0.8905
NW_003729277.1 3948 3555 0.9005 0.9039
NW_003729278.1 3941 4313 1.0944 1.0437
NW_003729279.1 3928 4002 1.0188 1.1896
NW_003729280.1 3925 3712 0.9457 0.9366
NW_003729281.1 3919 1800 0.4593 0.5623
NW_003729282.1 3849 3858 1.0023 1.09
NW_003729283.1 3848 2700 0.7017 0.7284
NW_003729284.1 3847 3818 0.9925 0.9113
NW_003729285.1 3817 4193 1.0985 1.0538
NW_003729286.1 3780 897 0.2373 0.4902
NW_003729287.1 3780 2080 0.5503 0.8673
NW_003729288.1 3777 2691 0.7125 0.7701
NW_003729289.1 3761 3266 0.8684 1.0044
NW_003729290.1 3750 4339 1.1571 1.0955
NW_003729291.1 3733 2377 0.6368 0.7404
NW_003729292.1 3719 3595 0.9667 0.7768
NW_003729293.1 3718 3430 0.9225 0.9805
NW_003729294.1 3706 3276 0.884 0.9396
NW_003729295.1 3700 4738 1.2805 1.6938
NW_003729296.1 3695 2969 0.8035 0.7987
NW_003729297.1 3652 4165 1.1405 1.1227
NW_003729298.1 3649 4143 1.1354 1.1561
NW_003729299.1 3629 3563 0.9818 0.9819
NW_003729300.1 3622 3890 1.074 1.0369
NW_003729301.1 3616 2988 0.8263 1.1184
NW_003729302.1 3614 3897 1.0783 1.261
NW_003729303.1 3595 4031 1.1213 0.9359
NW_003729304.1 3589 4155 1.1577 1.1035
NW_003729305.1 3585 3597 1.0033 0.7661
NW_003729306.1 3580 3284 0.9173 0.6971
NW_003729307.1 3576 4133 1.1558 1.0205
NW_003729308.1 3564 2690 0.7548 0.9128
NW_003729309.1 3524 3600 1.0216 0.7705
NW_003729310.1 3506 2971 0.8474 0.9225
NW_003729311.1 3484 3585 1.029 1.0097
NW_003729312.1 3480 3538 1.0167 1.1084
NW_003729313.1 3479 2074 0.5961 0.8357
NW_003729314.1 3440 3290 0.9564 1.173
NW_003729315.1 3431 3892 1.1344 0.9299
NW_003729316.1 3430 2374 0.6921 0.649
NW_003729317.1 3407 2379 0.6983 0.7892
NW_003729318.1 3398 2376 0.6992 0.7502
NW_003729319.1 3393 3868 1.14 1.1461
NW_003729320.1 3388 2542 0.7503 0.8636
NW_003729321.1 3369 1782 0.5289 0.7373
NW_003729322.1 3338 2987 0.8948 0.9218
NW_003729323.1 3331 2647 0.7947 0.8756
NW_003729324.1 3271 2989 0.9138 1.0394
NW_003729325.1 3257 2689 0.8256 1.0857
NW_003729326.1 3257 3285 1.0086 0.9654
NW_003729327.1 3231 3579 1.1077 1.2752
NW_003729328.1 3135 3574 1.14 1.1405
NW_003729329.1 3134 2966 0.9464 1.0917
NW_003729330.1 3059 2980 0.9742 0.9715
NW_003729331.1 3011 2989 0.9927 0.9722
NW_003729332.1 2997 3260 1.0878 0.8862
NW_003729333.1 2955 3590 1.2149 0.9797
NW_003729334.1 2933 1641 0.5595 0.7337
NW_003729335.1 2850 2693 0.9449 0.8157
NW_003729336.1 2823 2696 0.955 1.1385
NW_003729337.1 2809 1472 0.524 0.7786
NW_003729338.1 2772 2075 0.7486 0.7672
NW_003729339.1 2729 2677 0.9809 1.1239
NW_003729340.1 2708 2214 0.8176 0.7541
NW_003729341.1 2700 2844 1.0533 1.1672
NW_003729342.1 2641 3727 1.4112 1.0969
NW_003729343.1 2494 1482 0.5942 0.7163
NW_003729344.1 2361 2666 1.1292 1.0905
NW_003729345.1 2327 2090 0.8982 1.0482
NW_003729346.1 2250 1200 0.5333 0.672
NW_003729347.1 2145 2096 0.9772 0.8749
NW_003729348.1 2046 1788 0.8739 0.8736
NW_003729349.1 1999 1800 0.9005 1.2463
NW_003729350.1 1819 1496 0.8224 0.7768
NW_003729351.1 1790 900 0.5028 0.5621
NW_003729352.1 1685 1789 1.0617 0.8184
NW_003729353.1 1573 1800 1.1443 1.1805
NW_003729354.1 1115 900 0.8072 0.7679
NC_002008.4 16727 16762 1.0021 1.0882

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 17:32:15
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