Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/5X_haploid_no_error_med_variance/alignment/5X_haploid_no_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/5X_haploid_no_error_med_variance/5X_haploid_no_error_med_variance_R1.fa results/5X_haploid_no_error_med_variance/5X_haploid_no_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 18:01:01 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/5X_haploid_no_error_med_variance/alignment/5X_haploid_no_error_med_variance.sorted.bam

Summary 

Globals

Reference size 2,410,976,875
Number of reads 80,365,282
Mapped reads 80,365,282 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 80,365,282 / 100%
Mapped reads, first in pair 40,182,641 / 50%
Mapped reads, second in pair 40,182,641 / 50%
Mapped reads, both in pair 80,365,282 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Supplementary alignments 38 / 0%
Read min/max/mean length 30 / 150 / 150
Duplicated reads (estimated) 1,368,660 / 1.7%
Duplication rate 1.71%
Clipped reads 624,160 / 0.78%

ACGT Content

Number/percentage of A's 3,527,905,131 / 29.3%
Number/percentage of C's 2,492,234,787 / 20.7%
Number/percentage of T's 3,528,014,478 / 29.3%
Number/percentage of G's 2,492,068,018 / 20.7%
Number/percentage of N's 20,380 / 0%
GC Percentage 41.4%

Coverage

Mean 4.9989
Standard Deviation 2.3359

Mapping Quality

Mean Mapping Quality 31.86

Insert size

Mean 357.98
Standard Deviation 19,291.2
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 1.05%
Mismatches 114,432,619
Insertions 8,441,442
Mapped reads with at least one insertion 10%
Deletions 8,491,214
Mapped reads with at least one deletion 10.05%
Homopolymer indels 28.62%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 613844716 5.0037 2.3122
NC_006584.3 85426708 428376133 5.0145 2.316
NC_006585.3 91889043 459778061 5.0036 2.3013
NC_006586.3 88276631 441805941 5.0048 2.2977
NC_006587.3 88915250 444712130 5.0015 2.3066
NC_006588.3 77573801 388090694 5.0029 2.3242
NC_006589.3 80974532 404984785 5.0014 2.304
NC_006590.3 74330416 371691286 5.0005 2.3014
NC_006591.3 61074082 305804679 5.0071 2.325
NC_006592.3 69331447 346609742 4.9993 2.3134
NC_006593.3 74389097 371956969 5.0002 2.3001
NC_006594.3 72498081 362362600 4.9982 2.2949
NC_006595.3 63241923 316133490 4.9988 2.3033
NC_006596.3 60966679 304852192 5.0003 2.3006
NC_006597.3 64190966 320842972 4.9983 2.3155
NC_006598.3 59632846 298600373 5.0073 2.3265
NC_006599.3 64289059 321496056 5.0008 2.295
NC_006600.3 55844845 279257117 5.0006 2.3171
NC_006601.3 53741614 268651012 4.9989 2.2935
NC_006602.3 58134056 290581615 4.9985 2.3094
NC_006603.3 50858623 254239788 4.999 2.3065
NC_006604.3 61439934 307064776 4.9978 2.2924
NC_006605.3 52294480 261334015 4.9974 2.2913
NC_006606.3 47698779 238524879 5.0006 2.3075
NC_006607.3 51628933 258039160 4.998 2.3086
NC_006608.3 38964690 194940287 5.003 2.309
NC_006609.3 45876710 229240230 4.9969 2.2958
NC_006610.3 41182112 205836697 4.9982 2.3178
NC_006611.3 41845238 209097884 4.9969 2.2968
NC_006612.3 40214260 200999093 4.9982 2.3005
NC_006613.3 39895921 199417558 4.9984 2.2981
NC_006614.3 38810281 193974538 4.998 2.2882
NC_006615.3 31377067 156903337 5.0006 2.3085
NC_006616.3 42124431 210533120 4.9979 2.3054
NC_006617.3 26524999 132589686 4.9987 2.3029
NC_006618.3 30810995 154005705 4.9984 2.3031
NC_006619.3 30902991 154460718 4.9982 2.3127
NC_006620.3 23914537 119559371 4.9994 2.3177
NC_006621.3 123869142 619033342 4.9975 2.3117
NW_003726127.1 2660953 13351601 5.0176 2.4403
NW_003726128.1 1881673 9406700 4.9991 2.8403
NW_003726129.1 1415205 7092983 5.012 2.7714
NW_003726130.1 1067467 5344743 5.0069 3.0497
NW_003726131.1 866315 4368526 5.0427 2.3102
NW_003726132.1 881102 4456428 5.0578 2.7127
NW_003726133.1 822601 4118980 5.0073 2.5892
NW_003726134.1 741967 3716576 5.0091 2.271
NW_003726135.1 745551 3716515 4.9849 3.2638
NW_003726136.1 602611 3009360 4.9939 2.2664
NW_003726137.1 573630 2870865 5.0047 2.4166
NW_003726138.1 666183 3323770 4.9893 3.176
NW_003726139.1 557017 2807129 5.0396 2.6521
NW_003726140.1 510604 2574494 5.0421 2.3736
NW_003726141.1 497093 2516741 5.0629 2.4193
NW_003726142.1 492630 2446947 4.9671 2.5651
NW_003726143.1 577062 2880705 4.992 3.5066
NW_003726144.1 561270 2785681 4.9632 3.3858
NW_003726145.1 407330 2059511 5.0561 2.3369
NW_003726146.1 405216 2048549 5.0554 2.308
NW_003726147.1 508668 2542582 4.9985 3.5181
NW_003726148.1 540093 2674292 4.9515 4.0157
NW_003726149.1 448434 2223945 4.9594 3.2288
NW_003726150.1 377800 1878826 4.9731 2.4747
NW_003726151.1 384880 1924475 5.0002 2.7208
NW_003726152.1 367143 1843341 5.0208 2.4395
NW_003726153.1 399987 2011532 5.029 3.0197
NW_003726154.1 376204 1887267 5.0166 2.7063
NW_003726155.1 416178 2077262 4.9913 3.3355
NW_003726156.1 365470 1825917 4.9961 2.9299
NW_003726157.1 322752 1632385 5.0577 2.4117
NW_003726158.1 320591 1629091 5.0815 2.437
NW_003726159.1 310270 1552809 5.0047 2.4443
NW_003726160.1 433650 2169785 5.0035 4.0889
NW_003726161.1 273228 1366838 5.0026 2.3197
NW_003726162.1 281659 1415795 5.0266 2.509
NW_003726163.1 320442 1610943 5.0273 3.1989
NW_003726164.1 265648 1333908 5.0213 2.3316
NW_003726165.1 241365 1225503 5.0774 2.4008
NW_003726166.1 234529 1198172 5.1088 2.4326
NW_003726167.1 252720 1286863 5.0921 2.9043
NW_003726168.1 254975 1283192 5.0326 2.9738
NW_003726169.1 226053 1123254 4.969 2.3992
NW_003726170.1 223744 1135109 5.0732 2.3346
NW_003726171.1 227140 1137315 5.0071 2.4619
NW_003726172.1 219672 1094118 4.9807 2.3927
NW_003726173.1 214597 1088753 5.0735 2.3622
NW_003726174.1 386314 1925588 4.9845 5.205
NW_003726175.1 204342 1026597 5.0239 2.2743
NW_003726176.1 201724 1010869 5.0111 2.3652
NW_003726177.1 216332 1094418 5.059 2.7333
NW_003726178.1 200877 1011258 5.0342 2.2848
NW_003726179.1 310654 1504960 4.8445 4.3273
NW_003726180.1 200932 994117 4.9475 2.4436
NW_003726181.1 201410 1015753 5.0432 2.3549
NW_003726182.1 292533 1423693 4.8668 4.0987
NW_003726183.1 192561 971285 5.044 2.361
NW_003726184.1 210134 1067072 5.0781 2.9216
NW_003726185.1 197844 994908 5.0287 2.6996
NW_003726186.1 196813 1030792 5.2374 2.7403
NW_003726187.1 180359 911839 5.0557 2.3085
NW_003726188.1 210247 1002282 4.7672 3.1652
NW_003726189.1 177735 932754 5.248 2.4621
NW_003726190.1 172100 872366 5.0689 2.3592
NW_003726191.1 166866 835570 5.0074 2.3077
NW_003726192.1 164926 840316 5.0951 2.2851
NW_003726193.1 157598 776296 4.9258 2.6697
NW_003726194.1 143980 719803 4.9993 2.4132
NW_003726195.1 141074 701223 4.9706 2.4168
NW_003726196.1 139526 698202 5.0041 2.2855
NW_003726197.1 142260 731432 5.1415 2.4947
NW_003726198.1 138160 699684 5.0643 2.3126
NW_003726199.1 142296 723192 5.0823 2.5726
NW_003726200.1 133119 663432 4.9838 2.274
NW_003726201.1 129748 648630 4.9992 2.3097
NW_003726202.1 125962 644130 5.1137 2.3471
NW_003726203.1 127429 639417 5.0178 2.3441
NW_003726204.1 128261 643685 5.0186 2.5418
NW_003726205.1 131872 654985 4.9668 2.7448
NW_003726206.1 133432 680104 5.097 2.9227
NW_003726207.1 119670 609150 5.0902 2.2558
NW_003726208.1 144750 713969 4.9324 3.4076
NW_003726209.1 120779 611739 5.0649 2.5752
NW_003726210.1 115952 583149 5.0292 2.2036
NW_003726211.1 118237 567196 4.7971 2.5488
NW_003726212.1 111908 562462 5.0261 2.3499
NW_003726213.1 117332 611415 5.211 2.6625
NW_003726214.1 111759 558657 4.9988 2.3272
NW_003726215.1 108801 553373 5.0861 2.274
NW_003726216.1 112014 568439 5.0747 2.6042
NW_003726217.1 106428 547879 5.1479 2.341
NW_003726218.1 104912 525210 5.0062 2.4457
NW_003726219.1 104646 523787 5.0053 2.3558
NW_003726220.1 103248 516414 5.0017 2.3108
NW_003726221.1 129482 640858 4.9494 3.6441
NW_003726222.1 118473 587960 4.9628 3.0518
NW_003726223.1 99993 502086 5.0212 2.2947
NW_003726224.1 109585 556100 5.0746 2.7932
NW_003726225.1 124049 586256 4.726 3.2606
NW_003726226.1 99658 500486 5.022 2.4848
NW_003726227.1 101741 508409 4.9971 2.6658
NW_003726228.1 97365 485493 4.9863 2.2261
NW_003726229.1 94395 476445 5.0474 2.3485
NW_003726230.1 102992 497009 4.8257 2.8253
NW_003726231.1 95509 472740 4.9497 2.5605
NW_003726232.1 92047 459011 4.9867 2.4003
NW_003726233.1 87753 434341 4.9496 2.1977
NW_003726234.1 96536 477784 4.9493 3.0254
NW_003726235.1 86544 441816 5.1051 2.4753
NW_003726236.1 85476 423195 4.951 2.2508
NW_003726237.1 110512 535263 4.8435 3.7656
NW_003726238.1 83291 418208 5.021 2.3336
NW_003726239.1 82459 426740 5.1752 2.3897
NW_003726240.1 81605 420816 5.1567 2.5246
NW_003726241.1 82380 423215 5.1374 2.6267
NW_003726242.1 102198 483353 4.7296 3.5414
NW_003726243.1 82108 410060 4.9942 2.4184
NW_003726244.1 87041 429804 4.9379 2.735
NW_003726245.1 79722 397424 4.9851 2.2591
NW_003726246.1 230124 1129013 4.9061 7.307
NW_003726247.1 78357 392430 5.0082 2.3798
NW_003726248.1 256406 1264086 4.93 7.9408
NW_003726249.1 78050 392451 5.0282 2.3284
NW_003726250.1 81930 410436 5.0096 2.6033
NW_003726251.1 77100 391279 5.075 2.4503
NW_003726252.1 77130 383851 4.9767 2.2624
NW_003726253.1 79078 399584 5.053 2.607
NW_003726254.1 90550 456146 5.0375 3.4305
NW_003726255.1 82767 416884 5.0368 2.8638
NW_003726256.1 89070 404011 4.5359 3.1508
NW_003726257.1 97802 482613 4.9346 3.6692
NW_003726258.1 79712 398606 5.0006 2.8667
NW_003726259.1 79581 410574 5.1592 2.7767
NW_003726260.1 73720 374236 5.0765 2.3937
NW_003726261.1 97799 477831 4.8858 3.7939
NW_003726262.1 73171 368979 5.0427 2.2832
NW_003726263.1 104732 515868 4.9256 4.0061
NW_003726264.1 78935 374879 4.7492 2.7951
NW_003726265.1 72992 375528 5.1448 2.5477
NW_003726266.1 68721 347575 5.0578 2.1431
NW_003726267.1 73611 368585 5.0072 2.7423
NW_003726268.1 68272 341971 5.0089 2.1862
NW_003726269.1 79297 406348 5.1244 3.2189
NW_003726270.1 84443 413715 4.8993 3.4663
NW_003726271.1 80679 388638 4.8171 3.3747
NW_003726272.1 68834 343141 4.9851 2.4468
NW_003726273.1 67496 337619 5.0021 2.4255
NW_003726274.1 66523 338625 5.0903 2.4577
NW_003726275.1 67057 333968 4.9804 2.3177
NW_003726276.1 66195 334443 5.0524 2.2921
NW_003726277.1 87584 435486 4.9722 3.7
NW_003726278.1 84679 390494 4.6115 3.5151
NW_003726279.1 65840 327957 4.9811 2.2551
NW_003726280.1 65696 333230 5.0723 2.2014
NW_003726281.1 66021 329863 4.9963 2.4809
NW_003726282.1 67300 332773 4.9446 2.6179
NW_003726283.1 88153 415289 4.711 3.7865
NW_003726284.1 92437 461506 4.9927 4.2446
NW_003726285.1 70351 350536 4.9827 3.1104
NW_003726286.1 64646 334984 5.1818 2.5286
NW_003726287.1 69126 345978 5.005 2.8768
NW_003726288.1 227674 1038583 4.5617 7.9387
NW_003726289.1 64123 319152 4.9772 2.4889
NW_003726290.1 61944 309224 4.992 2.3871
NW_003726291.1 62414 317226 5.0826 2.4588
NW_003726292.1 61779 310440 5.025 2.2761
NW_003726293.1 90840 420681 4.631 4.1563
NW_003726294.1 61194 302568 4.9444 2.3695
NW_003726295.1 63245 316704 5.0076 2.5643
NW_003726296.1 60975 308484 5.0592 2.2434
NW_003726297.1 88336 432076 4.8913 4.1048
NW_003726298.1 62896 297593 4.7315 2.4641
NW_003726299.1 60346 306821 5.0844 2.2778
NW_003726300.1 70666 330861 4.682 3.0408
NW_003726301.1 71007 358468 5.0483 3.3689
NW_003726302.1 59879 297133 4.9622 2.1024
NW_003726303.1 59817 305427 5.106 2.3287
NW_003726304.1 66981 330731 4.9377 3.0142
NW_003726305.1 62805 311910 4.9663 2.6399
NW_003726306.1 68857 328403 4.7693 3.1842
NW_003726307.1 58149 290027 4.9877 2.3941
NW_003726308.1 84024 407168 4.8459 4.1878
NW_003726309.1 58658 306385 5.2232 2.5094
NW_003726310.1 65402 332667 5.0865 3.0557
NW_003726311.1 56534 285399 5.0483 2.4204
NW_003726312.1 59023 308890 5.2334 2.7768
NW_003726313.1 89903 347724 3.8678 3.8812
NW_003726314.1 54477 305706 5.6117 2.6328
NW_003726315.1 54307 273527 5.0367 2.3954
NW_003726316.1 69310 320981 4.6311 3.6836
NW_003726317.1 57210 284041 4.9649 2.8193
NW_003726318.1 57907 285248 4.926 2.9912
NW_003726319.1 53093 266221 5.0142 2.4176
NW_003726320.1 67358 308897 4.5859 3.4849
NW_003726321.1 54660 287944 5.2679 2.5943
NW_003726322.1 52548 266450 5.0706 2.1633
NW_003726323.1 52637 265333 5.0408 2.2657
NW_003726324.1 51964 262362 5.0489 2.2334
NW_003726325.1 51648 266802 5.1658 2.3039
NW_003726326.1 51582 268589 5.207 2.3196
NW_003726327.1 52288 282581 5.4043 2.7309
NW_003726328.1 50462 253798 5.0295 2.282
NW_003726329.1 50869 251599 4.946 2.2874
NW_003726330.1 53506 269852 5.0434 2.6637
NW_003726331.1 50005 251287 5.0252 2.2041
NW_003726332.1 84691 329250 3.8877 3.8372
NW_003726333.1 63256 314409 4.9704 3.533
NW_003726334.1 59752 303383 5.0774 3.3845
NW_003726335.1 68739 321461 4.6765 3.9672
NW_003726336.1 49027 243264 4.9618 2.4552
NW_003726337.1 49032 242596 4.9477 2.386
NW_003726338.1 57792 278951 4.8268 3.4377
NW_003726339.1 74646 330191 4.4234 4.1343
NW_003726340.1 48411 243741 5.0348 2.3622
NW_003726341.1 48200 248528 5.1562 2.2728
NW_003726342.1 75626 328312 4.3413 4.049
NW_003726343.1 48436 241673 4.9895 2.4279
NW_003726344.1 47485 232370 4.8935 2.397
NW_003726345.1 52731 258539 4.903 2.6999
NW_003726346.1 52367 260455 4.9736 3.0058
NW_003726347.1 46689 237468 5.0862 2.3813
NW_003726348.1 53681 269168 5.0142 3.1082
NW_003726349.1 73441 318480 4.3365 4.1898
NW_003726350.1 57620 281638 4.8879 3.322
NW_003726351.1 70154 323009 4.6043 4.407
NW_003726352.1 67100 307707 4.5858 4.0572
NW_003726353.1 48085 240935 5.0106 2.5735
NW_003726354.1 63970 314055 4.9094 4.0105
NW_003726355.1 45242 226488 5.0061 2.3237
NW_003726356.1 58859 250332 4.2531 3.2251
NW_003726357.1 45065 237205 5.2636 2.3892
NW_003726358.1 46098 247041 5.359 2.6182
NW_003726359.1 70370 271401 3.8568 3.7972
NW_003726360.1 46044 236359 5.1333 2.6094
NW_003726361.1 45518 234515 5.1521 2.6555
NW_003726362.1 47960 244066 5.0889 2.8743
NW_003726363.1 44571 223650 5.0178 2.4421
NW_003726364.1 84617 384847 4.5481 5.287
NW_003726365.1 51679 263923 5.107 3.2386
NW_003726366.1 48264 236645 4.9031 2.9145
NW_003726367.1 50939 241253 4.7361 2.9848
NW_003726368.1 72756 317045 4.3576 4.4164
NW_003726369.1 44216 217004 4.9078 2.4189
NW_003726370.1 43704 219254 5.0168 2.2466
NW_003726371.1 55991 257279 4.595 3.4665
NW_003726372.1 54329 241150 4.4387 3.2242
NW_003726373.1 44549 224301 5.0349 2.5162
NW_003726374.1 44306 230473 5.2018 2.5826
NW_003726375.1 60428 252537 4.1791 3.5581
NW_003726376.1 42803 213047 4.9774 2.1932
NW_003726377.1 90666 424455 4.6815 5.7898
NW_003726378.1 42461 211269 4.9756 2.1742
NW_003726379.1 46059 227381 4.9367 2.6647
NW_003726380.1 58391 276592 4.7369 3.8605
NW_003726381.1 69503 293382 4.2211 4.3
NW_003726382.1 41842 209958 5.0179 2.4144
NW_003726383.1 43189 229446 5.3126 2.646
NW_003726384.1 42168 210921 5.0019 2.3447
NW_003726385.1 41454 211885 5.1113 2.2897
NW_003726386.1 43681 211502 4.842 2.5176
NW_003726387.1 57311 264638 4.6176 3.915
NW_003726388.1 68304 291917 4.2738 4.0984
NW_003726389.1 57240 279188 4.8775 4.0669
NW_003726390.1 42861 218125 5.0891 2.702
NW_003726391.1 43424 209310 4.8201 2.48
NW_003726392.1 40931 204552 4.9975 2.3719
NW_003726393.1 41221 206459 5.0086 2.274
NW_003726394.1 41006 203413 4.9606 2.3936
NW_003726395.1 40763 215346 5.2829 2.4156
NW_003726396.1 46509 220719 4.7457 3.0587
NW_003726397.1 42743 212746 4.9773 2.8121
NW_003726398.1 40517 203260 5.0167 2.2259
NW_003726399.1 40818 202760 4.9674 2.4066
NW_003726400.1 45697 229446 5.021 3.1592
NW_003726401.1 46980 222288 4.7315 3.2364
NW_003726402.1 42806 221163 5.1666 2.8485
NW_003726403.1 44573 217719 4.8845 2.9692
NW_003726404.1 39716 197950 4.9841 2.4915
NW_003726405.1 39345 191382 4.8642 2.1594
NW_003726406.1 46145 230066 4.9857 3.0594
NW_003726407.1 47441 240125 5.0616 3.4244
NW_003726408.1 39138 195742 5.0013 2.1796
NW_003726409.1 40677 202793 4.9854 2.5153
NW_003726410.1 64983 299670 4.6115 4.5906
NW_003726411.1 51094 242525 4.7466 3.9158
NW_003726412.1 38580 203683 5.2795 2.6112
NW_003726413.1 40054 201484 5.0303 2.526
NW_003726414.1 39199 187178 4.7751 2.5365
NW_003726415.1 38084 189594 4.9783 2.3359
NW_003726416.1 41432 206658 4.9879 2.7182
NW_003726417.1 45027 222571 4.9431 3.3376
NW_003726418.1 37707 211249 5.6024 2.9631
NW_003726419.1 59547 281969 4.7352 4.2835
NW_003726420.1 58434 270590 4.6307 4.5371
NW_003726421.1 37389 183632 4.9114 2.2248
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NW_003729140.1 4726 20993 4.442 2.6462
NW_003729141.1 4725 22035 4.6635 2.1193
NW_003729142.1 4718 20674 4.3819 2.4691
NW_003729143.1 4717 22324 4.7327 2.249
NW_003729144.1 4702 23118 4.9166 2.1747
NW_003729145.1 4702 20966 4.459 2.36
NW_003729146.1 4698 21904 4.6624 2.582
NW_003729147.1 4695 23966 5.1046 2.3841
NW_003729148.1 4694 22213 4.7322 2.7335
NW_003729149.1 4689 28209 6.016 2.8474
NW_003729150.1 4688 24004 5.1203 2.3048
NW_003729151.1 4687 21853 4.6625 2.0752
NW_003729152.1 4685 23081 4.9266 2.4605
NW_003729153.1 4683 25504 5.4461 3.0494
NW_003729154.1 4681 22785 4.8675 2.6659
NW_003729155.1 4676 22483 4.8082 2.3236
NW_003729156.1 4673 18897 4.0439 2.1479
NW_003729157.1 4673 24903 5.3291 2.3638
NW_003729158.1 4669 22785 4.8801 2.1362
NW_003729159.1 4668 23838 5.1067 2.6374
NW_003729160.1 4662 24000 5.148 2.8474
NW_003729161.1 4659 25160 5.4003 1.9735
NW_003729162.1 4649 23676 5.0927 2.1606
NW_003729163.1 4649 25792 5.5479 2.7874
NW_003729164.1 4639 25105 5.4117 2.6064
NW_003729165.1 4636 22759 4.9092 2.608
NW_003729166.1 4631 20383 4.4014 2.219
NW_003729167.1 4630 20970 4.5292 2.3131
NW_003729168.1 4629 22189 4.7935 2.471
NW_003729169.1 4619 20386 4.4135 2.8955
NW_003729170.1 4613 20989 4.55 1.8861
NW_003729171.1 4612 23987 5.201 2.4647
NW_003729172.1 4601 23098 5.0202 2.4103
NW_003729173.1 4600 23114 5.0248 2.3518
NW_003729174.1 4600 20039 4.3563 2.4291
NW_003729175.1 4594 21560 4.6931 2.5217
NW_003729176.1 4588 21311 4.6449 2.0121
NW_003729177.1 4580 22350 4.8799 1.9914
NW_003729178.1 4577 22493 4.9144 2.3421
NW_003729179.1 4577 23098 5.0465 2.8767
NW_003729180.1 4577 22965 5.0175 2.315
NW_003729181.1 4575 21273 4.6498 2.5585
NW_003729182.1 4574 24860 5.4351 2.1947
NW_003729183.1 4572 24595 5.3795 2.4188
NW_003729184.1 4572 23741 5.1927 2.5005
NW_003729185.1 4562 20977 4.5982 2.4603
NW_003729186.1 4555 21569 4.7352 2.3286
NW_003729187.1 4554 21326 4.6829 2.4684
NW_003729188.1 4552 19782 4.3458 2.4011
NW_003729189.1 4550 24012 5.2774 2.605
NW_003729190.1 4543 18885 4.1569 2.1871
NW_003729191.1 4541 23099 5.0868 2.9866
NW_003729192.1 4539 24007 5.2891 2.8515
NW_003729193.1 4527 20387 4.5034 3.1618
NW_003729194.1 4519 22778 5.0405 2.591
NW_003729195.1 4507 22485 4.9889 2.0978
NW_003729196.1 4501 20383 4.5285 2.4614
NW_003729197.1 4485 21601 4.8163 2.2405
NW_003729198.1 4480 20088 4.4839 2.4021
NW_003729199.1 4476 23371 5.2214 2.6967
NW_003729200.1 4469 25759 5.7639 3.3784
NW_003729201.1 4463 22789 5.1062 2.979
NW_003729202.1 4460 19762 4.4309 2.8217
NW_003729203.1 4454 23397 5.253 2.2985
NW_003729204.1 4453 22490 5.0505 2.2359
NW_003729205.1 4447 21912 4.9274 2.832
NW_003729206.1 4443 24602 5.5372 2.6106
NW_003729207.1 4439 22201 5.0014 2.6285
NW_003729208.1 4437 19761 4.4537 2.629
NW_003729209.1 4430 23424 5.2876 2.5832
NW_003729210.1 4429 22785 5.1445 2.2589
NW_003729211.1 4428 19806 4.4729 1.9979
NW_003729212.1 4420 20978 4.7462 2.7299
NW_003729213.1 4418 24586 5.565 2.4144
NW_003729214.1 4418 19476 4.4083 2.0457
NW_003729215.1 4408 21597 4.8995 2.2775
NW_003729216.1 4404 26107 5.928 2.1582
NW_003729217.1 4404 21003 4.7691 2.2705
NW_003729218.1 4403 21880 4.9693 2.8379
NW_003729219.1 4399 23252 5.2857 2.5317
NW_003729220.1 4393 21883 4.9813 2.491
NW_003729221.1 4389 22817 5.1987 2.3158
NW_003729222.1 4389 25047 5.7068 2.8095
NW_003729223.1 4388 19497 4.4433 3.0316
NW_003729224.1 4378 24859 5.6782 2.7967
NW_003729225.1 4368 21602 4.9455 2.4453
NW_003729226.1 4359 24278 5.5696 2.987
NW_003729227.1 4356 23055 5.2927 2.5229
NW_003729228.1 4353 20648 4.7434 1.9687
NW_003729229.1 4329 19758 4.5641 1.7789
NW_003729230.1 4311 19496 4.5224 2.1935
NW_003729231.1 4302 17659 4.1048 2.4524
NW_003729232.1 4300 22473 5.2263 2.6942
NW_003729233.1 4285 20958 4.891 1.9933
NW_003729234.1 4283 18253 4.2617 2.734
NW_003729235.1 4282 21294 4.9729 2.6804
NW_003729236.1 4281 21287 4.9724 2.2478
NW_003729237.1 4279 20970 4.9007 2.2929
NW_003729238.1 4277 20963 4.9013 2.3838
NW_003729239.1 4276 19467 4.5526 2.3419
NW_003729240.1 4276 22495 5.2608 2.1585
NW_003729241.1 4252 18902 4.4454 2.3504
NW_003729242.1 4248 21854 5.1445 2.7565
NW_003729243.1 4239 21872 5.1597 2.1928
NW_003729244.1 4238 20692 4.8825 2.9203
NW_003729245.1 4234 20399 4.8179 2.4365
NW_003729246.1 4233 20996 4.9601 2.7825
NW_003729247.1 4231 20104 4.7516 2.4875
NW_003729248.1 4225 16929 4.0069 2.7128
NW_003729249.1 4201 21554 5.1307 2.167
NW_003729250.1 4198 22149 5.2761 2.3297
NW_003729251.1 4193 20072 4.787 2.2373
NW_003729252.1 4186 20703 4.9458 2.267
NW_003729253.1 4183 19489 4.6591 2.5387
NW_003729254.1 4177 17384 4.1618 1.9762
NW_003729255.1 4172 19179 4.5971 1.8485
NW_003729256.1 4163 20980 5.0396 2.5796
NW_003729257.1 4156 20409 4.9107 2.0947
NW_003729258.1 4141 18580 4.4868 2.5841
NW_003729259.1 4130 20692 5.0102 2.0871
NW_003729260.1 4130 21742 5.2644 3.5083
NW_003729261.1 4126 25790 6.2506 2.8645
NW_003729262.1 4123 21314 5.1695 2.088
NW_003729263.1 4121 21287 5.1655 2.5613
NW_003729264.1 4117 20660 5.0182 1.9091
NW_003729265.1 4112 20390 4.9587 2.4187
NW_003729266.1 4097 22487 5.4887 2.1312
NW_003729267.1 4096 17853 4.3586 2.1797
NW_003729268.1 4070 16195 3.9791 2.3267
NW_003729269.1 4064 20652 5.0817 2.805
NW_003729270.1 4061 19203 4.7286 2.6152
NW_003729271.1 4060 15885 3.9126 1.8663
NW_003729272.1 4025 21313 5.2952 3.0074
NW_003729273.1 4025 20956 5.2065 2.6941
NW_003729274.1 4011 21924 5.466 2.7532
NW_003729275.1 4001 19793 4.947 2.3116
NW_003729276.1 3976 20072 5.0483 2.481
NW_003729277.1 3948 18335 4.6441 3.1938
NW_003729278.1 3941 23081 5.8566 2.222
NW_003729279.1 3928 20416 5.1976 2.4993
NW_003729280.1 3925 15891 4.0487 2.1877
NW_003729281.1 3919 20681 5.2771 2.4623
NW_003729282.1 3849 16494 4.2853 2.977
NW_003729283.1 3848 19811 5.1484 1.9945
NW_003729284.1 3847 18690 4.8583 2.1816
NW_003729285.1 3817 18602 4.8735 2.4487
NW_003729286.1 3780 16498 4.3646 2.4099
NW_003729287.1 3780 19192 5.0772 3.3343
NW_003729288.1 3777 16805 4.4493 1.9462
NW_003729289.1 3761 16478 4.3813 2.5822
NW_003729290.1 3750 16217 4.3245 2.4234
NW_003729291.1 3733 17643 4.7262 3.0505
NW_003729292.1 3719 16335 4.3923 2.1362
NW_003729293.1 3718 20728 5.575 2.5433
NW_003729294.1 3706 19334 5.2169 2.731
NW_003729295.1 3700 17111 4.6246 2.4143
NW_003729296.1 3695 18271 4.9448 2.576
NW_003729297.1 3652 16505 4.5194 2.3132
NW_003729298.1 3649 16160 4.4286 2.2395
NW_003729299.1 3629 18437 5.0805 2.5395
NW_003729300.1 3622 18011 4.9727 2.6063
NW_003729301.1 3616 15860 4.3861 2.433
NW_003729302.1 3614 14289 3.9538 2.3577
NW_003729303.1 3595 19458 5.4125 2.9969
NW_003729304.1 3589 18256 5.0867 2.5368
NW_003729305.1 3585 16780 4.6806 2.724
NW_003729306.1 3580 17094 4.7749 2.7525
NW_003729307.1 3576 15292 4.2763 2.6705
NW_003729308.1 3564 18897 5.3022 2.4821
NW_003729309.1 3524 18003 5.1087 2.1222
NW_003729310.1 3506 16512 4.7096 1.908
NW_003729311.1 3484 18303 5.2534 2.366
NW_003729312.1 3480 15286 4.3925 2.5022
NW_003729313.1 3479 19800 5.6913 2.3957
NW_003729314.1 3440 18593 5.4049 2.4587
NW_003729315.1 3431 18282 5.3285 2.2279
NW_003729316.1 3430 17087 4.9816 2.8447
NW_003729317.1 3407 17976 5.2762 2.0364
NW_003729318.1 3398 16804 4.9453 2.5449
NW_003729319.1 3393 16157 4.7619 2.5912
NW_003729320.1 3388 16495 4.8687 2.8211
NW_003729321.1 3369 12885 3.8246 3.0474
NW_003729322.1 3338 15295 4.5821 2.8498
NW_003729323.1 3331 16806 5.0453 2.1222
NW_003729324.1 3271 15908 4.8633 2.2943
NW_003729325.1 3257 16055 4.9294 2.4634
NW_003729326.1 3257 16201 4.9742 1.83
NW_003729327.1 3231 12583 3.8945 2.5274
NW_003729328.1 3135 16353 5.2163 3.8434
NW_003729329.1 3134 15279 4.8752 2.9707
NW_003729330.1 3059 15001 4.9039 2.203
NW_003729331.1 3011 17386 5.7742 2.5216
NW_003729332.1 2997 12873 4.2953 2.2917
NW_003729333.1 2955 14347 4.8552 3.2764
NW_003729334.1 2933 12597 4.2949 2.0812
NW_003729335.1 2850 13498 4.7361 2.7475
NW_003729336.1 2823 15015 5.3188 2.494
NW_003729337.1 2809 8111 2.8875 2.2081
NW_003729338.1 2772 9000 3.2468 2.0596
NW_003729339.1 2729 13533 4.959 2.2603
NW_003729340.1 2708 12003 4.4324 1.8539
NW_003729341.1 2700 12909 4.7811 2.5008
NW_003729342.1 2641 12007 4.5464 3.1522
NW_003729343.1 2494 12028 4.8228 2.4144
NW_003729344.1 2361 12295 5.2075 2.8031
NW_003729345.1 2327 12915 5.5501 2.4878
NW_003729346.1 2250 10477 4.6564 2.3557
NW_003729347.1 2145 10784 5.0275 2.8875
NW_003729348.1 2046 9903 4.8402 1.7454
NW_003729349.1 1999 8114 4.059 2.0195
NW_003729350.1 1819 9903 5.4442 3.1667
NW_003729351.1 1790 8088 4.5184 2.6757
NW_003729352.1 1685 8402 4.9864 3.1899
NW_003729353.1 1573 4194 2.6662 1.702
NW_003729354.1 1115 4489 4.026 2.397
NC_002008.4 16727 83683 5.0029 2.2714

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 18:01:02
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