Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam results/5X_no_error_med_variance/alignment/5X_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_no_error_med_variance/5X_no_error_med_variance_R1.fa results/5X_no_error_med_variance/5X_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 17:54:38 PDT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: results/5X_no_error_med_variance/alignment/5X_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 17 / 0%
Read min/max/mean length 30 / 150 / 150
Duplicated reads (estimated) 1,352,181 / 1.68%
Duplication rate 1.69%
Clipped reads 375,225 / 0.47%

ACGT Content

Number/percentage of A's 3,531,503,785 / 29.32%
Number/percentage of C's 2,491,175,445 / 20.68%
Number/percentage of T's 3,531,492,036 / 29.32%
Number/percentage of G's 2,491,144,289 / 20.68%
Number/percentage of N's 20,948 / 0%
GC Percentage 41.36%

Coverage

Mean 4.9994
Standard Deviation 2.3329

Mapping Quality

Mean Mapping Quality 32.07

Insert size

Mean 351.19
Standard Deviation 5,631.16
P25/Median/P75 316 / 350 / 384

Mismatches and indels

General error rate 0.7%
Mismatches 76,391,962
Insertions 5,651,958
Mapped reads with at least one insertion 6.81%
Deletions 5,683,765
Mapped reads with at least one deletion 6.84%
Homopolymer indels 28.71%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
NC_006583.3 122678785 613957896 5.0046 2.3099
NC_006584.3 85426708 428432882 5.0152 2.3167
NC_006585.3 91889043 459759741 5.0034 2.2944
NC_006586.3 88276631 441834927 5.0051 2.2942
NC_006587.3 88915250 444745835 5.0019 2.3029
NC_006588.3 77573801 388083855 5.0028 2.3185
NC_006589.3 80974532 404934967 5.0008 2.3018
NC_006590.3 74330416 371701955 5.0007 2.2958
NC_006591.3 61074082 305818834 5.0073 2.3209
NC_006592.3 69331447 346594702 4.9991 2.3144
NC_006593.3 74389097 372028649 5.0011 2.2962
NC_006594.3 72498081 362380264 4.9985 2.2896
NC_006595.3 63241923 316202870 4.9999 2.3029
NC_006596.3 60966679 304871180 5.0006 2.3008
NC_006597.3 64190966 320889224 4.999 2.3111
NC_006598.3 59632846 298590885 5.0072 2.3228
NC_006599.3 64289059 321609938 5.0026 2.2922
NC_006600.3 55844845 279302053 5.0014 2.3174
NC_006601.3 53741614 268673380 4.9994 2.2873
NC_006602.3 58134056 290572200 4.9983 2.3122
NC_006603.3 50858623 254280748 4.9998 2.2992
NC_006604.3 61439934 307064955 4.9978 2.2892
NC_006605.3 52294480 261393169 4.9985 2.2862
NC_006606.3 47698779 238528518 5.0007 2.3051
NC_006607.3 51628933 258120740 4.9995 2.3054
NC_006608.3 38964690 194926973 5.0027 2.3045
NC_006609.3 45876710 229281823 4.9978 2.2986
NC_006610.3 41182112 205857291 4.9987 2.3073
NC_006611.3 41845238 209154990 4.9983 2.2933
NC_006612.3 40214260 201030980 4.999 2.2973
NC_006613.3 39895921 199453010 4.9993 2.2988
NC_006614.3 38810281 193993359 4.9985 2.2845
NC_006615.3 31377067 156888641 5.0001 2.3075
NC_006616.3 42124431 210581829 4.999 2.3022
NC_006617.3 26524999 132586486 4.9985 2.3027
NC_006618.3 30810995 154026308 4.9991 2.2972
NC_006619.3 30902991 154454209 4.998 2.3015
NC_006620.3 23914537 119542438 4.9987 2.3101
NC_006621.3 123869142 619062160 4.9977 2.3137
NW_003726127.1 2660953 13325627 5.0078 2.45
NW_003726128.1 1881673 9404957 4.9982 2.8697
NW_003726129.1 1415205 7092905 5.0119 2.726
NW_003726130.1 1067467 5345133 5.0073 3.0801
NW_003726131.1 866315 4341908 5.0119 2.3037
NW_003726132.1 881102 4458803 5.0605 2.7131
NW_003726133.1 822601 4152994 5.0486 2.6642
NW_003726134.1 741967 3713316 5.0047 2.2816
NW_003726135.1 745551 3710295 4.9766 3.2776
NW_003726136.1 602611 3021467 5.014 2.3398
NW_003726137.1 573630 2875090 5.0121 2.408
NW_003726138.1 666183 3313821 4.9743 3.1994
NW_003726139.1 557017 2806923 5.0392 2.6528
NW_003726140.1 510604 2591413 5.0752 2.2885
NW_003726141.1 497093 2492879 5.0149 2.4177
NW_003726142.1 492630 2461066 4.9958 2.5374
NW_003726143.1 577062 2884010 4.9977 3.4856
NW_003726144.1 561270 2797576 4.9844 3.4113
NW_003726145.1 407330 2053252 5.0408 2.294
NW_003726146.1 405216 2041449 5.0379 2.2681
NW_003726147.1 508668 2540709 4.9948 3.4617
NW_003726148.1 540093 2706164 5.0106 4.056
NW_003726149.1 448434 2236224 4.9867 3.2296
NW_003726150.1 377800 1896665 5.0203 2.5349
NW_003726151.1 384880 1939473 5.0392 2.7035
NW_003726152.1 367143 1842621 5.0188 2.4238
NW_003726153.1 399987 2019248 5.0483 3.0531
NW_003726154.1 376204 1883361 5.0062 2.7412
NW_003726155.1 416178 2075277 4.9865 3.3111
NW_003726156.1 365470 1823659 4.9899 2.9416
NW_003726157.1 322752 1633341 5.0607 2.3198
NW_003726158.1 320591 1633189 5.0943 2.4039
NW_003726159.1 310270 1552548 5.0039 2.4806
NW_003726160.1 433650 2133152 4.9191 4.0234
NW_003726161.1 273228 1378685 5.0459 2.2424
NW_003726162.1 281659 1418815 5.0374 2.5408
NW_003726163.1 320442 1606410 5.0131 3.1878
NW_003726164.1 265648 1336140 5.0297 2.3308
NW_003726165.1 241365 1239144 5.1339 2.4261
NW_003726166.1 234529 1201278 5.1221 2.3988
NW_003726167.1 252720 1290494 5.1064 2.8593
NW_003726168.1 254975 1275587 5.0028 3.0034
NW_003726169.1 226053 1132331 5.0091 2.3735
NW_003726170.1 223744 1135407 5.0746 2.3406
NW_003726171.1 227140 1144330 5.038 2.4696
NW_003726172.1 219672 1096912 4.9934 2.3797
NW_003726173.1 214597 1086874 5.0647 2.3407
NW_003726174.1 386314 1923981 4.9804 5.1927
NW_003726175.1 204342 1029423 5.0377 2.3637
NW_003726176.1 201724 1010703 5.0103 2.2584
NW_003726177.1 216332 1079401 4.9896 2.7045
NW_003726178.1 200877 1006944 5.0127 2.3065
NW_003726179.1 310654 1509117 4.8579 4.3102
NW_003726180.1 200932 1004572 4.9996 2.4237
NW_003726181.1 201410 1011474 5.022 2.4052
NW_003726182.1 292533 1431809 4.8945 4.1153
NW_003726183.1 192561 968960 5.032 2.2938
NW_003726184.1 210134 1074083 5.1114 2.8258
NW_003726185.1 197844 994362 5.026 2.6796
NW_003726186.1 196813 1006581 5.1144 2.8356
NW_003726187.1 180359 907759 5.0331 2.2285
NW_003726188.1 210247 1006443 4.787 3.1902
NW_003726189.1 177735 917641 5.163 2.5095
NW_003726190.1 172100 868486 5.0464 2.3348
NW_003726191.1 166866 849307 5.0898 2.433
NW_003726192.1 164926 846998 5.1356 2.4869
NW_003726193.1 157598 796221 5.0522 2.7858
NW_003726194.1 143980 719717 4.9987 2.4836
NW_003726195.1 141074 703309 4.9854 2.2196
NW_003726196.1 139526 701856 5.0303 2.3231
NW_003726197.1 142260 713800 5.0176 2.4286
NW_003726198.1 138160 697962 5.0518 2.3184
NW_003726199.1 142296 714196 5.0191 2.497
NW_003726200.1 133119 664859 4.9945 2.2825
NW_003726201.1 129748 648554 4.9986 2.2264
NW_003726202.1 125962 650829 5.1669 2.3416
NW_003726203.1 127429 640154 5.0236 2.3741
NW_003726204.1 128261 641732 5.0033 2.4699
NW_003726205.1 131872 653420 4.955 2.7016
NW_003726206.1 133432 684872 5.1327 2.9343
NW_003726207.1 119670 609656 5.0945 2.192
NW_003726208.1 144750 707756 4.8895 3.4153
NW_003726209.1 120779 610471 5.0544 2.5524
NW_003726210.1 115952 585130 5.0463 2.2833
NW_003726211.1 118237 561201 4.7464 2.554
NW_003726212.1 111908 554200 4.9523 2.3606
NW_003726213.1 117332 616117 5.2511 2.7236
NW_003726214.1 111759 558886 5.0008 2.3691
NW_003726215.1 108801 564149 5.1851 2.3947
NW_003726216.1 112014 570037 5.089 2.638
NW_003726217.1 106428 539148 5.0658 2.3677
NW_003726218.1 104912 524348 4.998 2.3768
NW_003726219.1 104646 528036 5.0459 2.2041
NW_003726220.1 103248 517357 5.0108 2.3934
NW_003726221.1 129482 638186 4.9288 3.6022
NW_003726222.1 118473 594276 5.0161 3.191
NW_003726223.1 99993 511119 5.1115 2.3548
NW_003726224.1 109585 541183 4.9385 2.8389
NW_003726225.1 124049 612158 4.9348 3.3912
NW_003726226.1 99658 507818 5.0956 2.402
NW_003726227.1 101741 508844 5.0014 2.6982
NW_003726228.1 97365 485571 4.9871 2.3105
NW_003726229.1 94395 478151 5.0654 2.4309
NW_003726230.1 102992 479008 4.6509 2.8494
NW_003726231.1 95509 476544 4.9895 2.4921
NW_003726232.1 92047 467909 5.0834 2.3773
NW_003726233.1 87753 448123 5.1066 2.357
NW_003726234.1 96536 458895 4.7536 3.0462
NW_003726235.1 86544 436108 5.0391 2.3482
NW_003726236.1 85476 429220 5.0215 2.2356
NW_003726237.1 110512 553767 5.0109 3.7798
NW_003726238.1 83291 416346 4.9987 2.2706
NW_003726239.1 82459 419087 5.0824 2.2554
NW_003726240.1 81605 427238 5.2354 2.4591
NW_003726241.1 82380 425270 5.1623 2.5691
NW_003726242.1 102198 480794 4.7045 3.5738
NW_003726243.1 82108 412142 5.0195 2.415
NW_003726244.1 87041 437087 5.0216 2.7487
NW_003726245.1 79722 408510 5.1242 2.2568
NW_003726246.1 230124 1134254 4.9289 7.3489
NW_003726247.1 78357 392353 5.0072 2.3922
NW_003726248.1 256406 1263118 4.9262 7.9356
NW_003726249.1 78050 402869 5.1617 2.4221
NW_003726250.1 81930 418556 5.1087 2.6907
NW_003726251.1 77100 387488 5.0258 2.2648
NW_003726252.1 77130 383658 4.9742 2.3894
NW_003726253.1 79078 400135 5.06 2.5876
NW_003726254.1 90550 427777 4.7242 3.2235
NW_003726255.1 82767 413851 5.0002 2.9601
NW_003726256.1 89070 394712 4.4315 2.9929
NW_003726257.1 97802 486216 4.9714 3.6338
NW_003726258.1 79712 398220 4.9957 2.896
NW_003726259.1 79581 404564 5.0837 2.8047
NW_003726260.1 73720 375043 5.0874 2.3497
NW_003726261.1 97799 479766 4.9056 3.7594
NW_003726262.1 73171 370073 5.0576 2.2788
NW_003726263.1 104732 522537 4.9893 4.0536
NW_003726264.1 78935 381569 4.834 2.7765
NW_003726265.1 72992 382154 5.2356 2.4072
NW_003726266.1 68721 343730 5.0018 2.191
NW_003726267.1 73611 366017 4.9723 2.6721
NW_003726268.1 68272 341654 5.0043 2.2738
NW_003726269.1 79297 398566 5.0262 3.3259
NW_003726270.1 84443 420040 4.9742 3.4197
NW_003726271.1 80679 384820 4.7698 3.3285
NW_003726272.1 68834 345396 5.0178 2.4763
NW_003726273.1 67496 337492 5.0002 2.4473
NW_003726274.1 66523 333608 5.0149 2.2953
NW_003726275.1 67057 333841 4.9785 2.3218
NW_003726276.1 66195 324018 4.8949 2.3797
NW_003726277.1 87584 430278 4.9127 3.6542
NW_003726278.1 84679 379774 4.4849 3.3056
NW_003726279.1 65840 329660 5.007 2.2674
NW_003726280.1 65696 331190 5.0413 2.2497
NW_003726281.1 66021 329736 4.9944 2.3807
NW_003726282.1 67300 336861 5.0054 2.5582
NW_003726283.1 88153 411294 4.6657 3.8882
NW_003726284.1 92437 451743 4.887 4.0413
NW_003726285.1 70351 346518 4.9256 2.9422
NW_003726286.1 64646 338677 5.2389 2.5895
NW_003726287.1 69126 343323 4.9666 2.904
NW_003726288.1 227674 1019563 4.4782 7.735
NW_003726289.1 64123 320968 5.0055 2.414
NW_003726290.1 61944 306883 4.9542 2.2223
NW_003726291.1 62414 313048 5.0157 2.3356
NW_003726292.1 61779 312845 5.0639 2.268
NW_003726293.1 90840 421973 4.6452 4.1662
NW_003726294.1 61194 310469 5.0735 2.2904
NW_003726295.1 63245 314914 4.9793 2.5106
NW_003726296.1 60975 307144 5.0372 2.2159
NW_003726297.1 88336 428326 4.8488 4.114
NW_003726298.1 62896 299656 4.7643 2.4954
NW_003726299.1 60346 301892 5.0027 2.0866
NW_003726300.1 70666 343880 4.8663 3.232
NW_003726301.1 71007 366694 5.1642 3.4868
NW_003726302.1 59879 298171 4.9796 2.1953
NW_003726303.1 59817 311064 5.2003 2.4508
NW_003726304.1 66981 327186 4.8848 3.0413
NW_003726305.1 62805 314077 5.0008 2.8323
NW_003726306.1 68857 335895 4.8782 3.2769
NW_003726307.1 58149 297530 5.1167 2.3118
NW_003726308.1 84024 409492 4.8735 4.1891
NW_003726309.1 58658 298217 5.084 2.553
NW_003726310.1 65402 328610 5.0245 3.132
NW_003726311.1 56534 278624 4.9284 2.3723
NW_003726312.1 59023 295128 5.0002 2.6524
NW_003726313.1 89903 377023 4.1937 4.3878
NW_003726314.1 54477 314451 5.7722 2.8708
NW_003726315.1 54307 272062 5.0097 2.357
NW_003726316.1 69310 326316 4.7081 3.6913
NW_003726317.1 57210 282545 4.9387 2.8057
NW_003726318.1 57907 293693 5.0718 2.9064
NW_003726319.1 53093 271175 5.1075 2.4354
NW_003726320.1 67358 302477 4.4906 3.4249
NW_003726321.1 54660 276929 5.0664 2.6149
NW_003726322.1 52548 275378 5.2405 2.4389
NW_003726323.1 52637 267293 5.078 2.2575
NW_003726324.1 51964 257668 4.9586 2.2455
NW_003726325.1 51648 255277 4.9426 2.3434
NW_003726326.1 51582 268418 5.2037 2.3469
NW_003726327.1 52288 267943 5.1244 2.3623
NW_003726328.1 50462 251081 4.9756 2.4424
NW_003726329.1 50869 256540 5.0432 2.488
NW_003726330.1 53506 273566 5.1128 2.7444
NW_003726331.1 50005 250531 5.0101 2.256
NW_003726332.1 84691 332958 3.9314 3.8648
NW_003726333.1 63256 320952 5.0739 3.5248
NW_003726334.1 59752 297485 4.9787 3.2273
NW_003726335.1 68739 309899 4.5083 3.8218
NW_003726336.1 49027 241739 4.9307 2.2755
NW_003726337.1 49032 245667 5.0103 2.4007
NW_003726338.1 57792 260961 4.5155 3.2219
NW_003726339.1 74646 330272 4.4245 4.1509
NW_003726340.1 48411 239617 4.9496 2.3888
NW_003726341.1 48200 244775 5.0783 2.1691
NW_003726342.1 75626 337355 4.4608 4.3556
NW_003726343.1 48436 238883 4.9319 2.3554
NW_003726344.1 47485 237277 4.9969 2.2154
NW_003726345.1 52731 256864 4.8712 2.8777
NW_003726346.1 52367 263896 5.0394 2.8766
NW_003726347.1 46689 231900 4.9669 2.1371
NW_003726348.1 53681 268760 5.0066 3.0799
NW_003726349.1 73441 327537 4.4599 4.2762
NW_003726350.1 57620 280984 4.8765 3.2384
NW_003726351.1 70154 315144 4.4922 4.2816
NW_003726352.1 67100 287070 4.2782 3.8302
NW_003726353.1 48085 240667 5.005 2.6054
NW_003726354.1 63970 304623 4.762 3.7731
NW_003726355.1 45242 226124 4.9981 2.3468
NW_003726356.1 58859 251631 4.2751 3.3544
NW_003726357.1 45065 223773 4.9656 2.4033
NW_003726358.1 46098 245699 5.3299 2.6752
NW_003726359.1 70370 279222 3.9679 3.8493
NW_003726360.1 46044 237279 5.1533 2.4625
NW_003726361.1 45518 222828 4.8954 2.3668
NW_003726362.1 47960 249523 5.2027 2.9559
NW_003726363.1 44571 222858 5.0001 2.3389
NW_003726364.1 84617 390254 4.612 5.1204
NW_003726365.1 51679 263144 5.0919 3.244
NW_003726366.1 48264 234245 4.8534 2.8301
NW_003726367.1 50939 240269 4.7168 2.945
NW_003726368.1 72756 314655 4.3248 4.4507
NW_003726369.1 44216 222008 5.021 2.4135
NW_003726370.1 43704 218440 4.9982 2.1939
NW_003726371.1 55991 260103 4.6454 3.5601
NW_003726372.1 54329 239662 4.4113 3.2658
NW_003726373.1 44549 226442 5.083 2.4626
NW_003726374.1 44306 230746 5.208 2.6178
NW_003726375.1 60428 258571 4.279 3.7807
NW_003726376.1 42803 210630 4.9209 2.4153
NW_003726377.1 90666 426619 4.7054 5.8448
NW_003726378.1 42461 209305 4.9293 2.143
NW_003726379.1 46059 227693 4.9435 2.7603
NW_003726380.1 58391 296386 5.0759 4.1145
NW_003726381.1 69503 290360 4.1777 4.1454
NW_003726382.1 41842 214212 5.1195 2.4083
NW_003726383.1 43189 224868 5.2066 2.5805
NW_003726384.1 42168 215410 5.1084 2.4767
NW_003726385.1 41454 209720 5.0591 2.4021
NW_003726386.1 43681 215401 4.9312 2.5553
NW_003726387.1 57311 271461 4.7366 3.9449
NW_003726388.1 68304 292402 4.2809 4.0797
NW_003726389.1 57240 278045 4.8575 4.1393
NW_003726390.1 42861 222531 5.1919 2.7123
NW_003726391.1 43424 211732 4.8759 2.5614
NW_003726392.1 40931 202719 4.9527 2.3274
NW_003726393.1 41221 202887 4.9219 2.3444
NW_003726394.1 41006 203661 4.9666 2.3404
NW_003726395.1 40763 206696 5.0707 2.5342
NW_003726396.1 46509 225897 4.8571 3.0516
NW_003726397.1 42743 216508 5.0653 2.726
NW_003726398.1 40517 207837 5.1296 2.2832
NW_003726399.1 40818 203132 4.9765 2.3055
NW_003726400.1 45697 237431 5.1958 3.0996
NW_003726401.1 46980 216239 4.6028 3.034
NW_003726402.1 42806 220231 5.1449 2.8129
NW_003726403.1 44573 228521 5.1269 3.0956
NW_003726404.1 39716 199533 5.024 2.0633
NW_003726405.1 39345 191442 4.8657 2.1503
NW_003726406.1 46145 224418 4.8633 3.0506
NW_003726407.1 47441 231270 4.8749 3.2349
NW_003726408.1 39138 201860 5.1576 2.2098
NW_003726409.1 40677 204019 5.0156 2.5996
NW_003726410.1 64983 298576 4.5947 4.6437
NW_003726411.1 51094 235143 4.6022 3.6859
NW_003726412.1 38580 196503 5.0934 2.391
NW_003726413.1 40054 202789 5.0629 2.6091
NW_003726414.1 39199 196712 5.0183 2.6977
NW_003726415.1 38084 191745 5.0348 2.5042
NW_003726416.1 41432 206989 4.9959 2.9905
NW_003726417.1 45027 206714 4.5909 3.3243
NW_003726418.1 37707 214253 5.682 2.8467
NW_003726419.1 59547 284246 4.7735 4.26
NW_003726420.1 58434 278817 4.7715 4.6853
NW_003726421.1 37389 182969 4.8937 2.2804
NW_003726422.1 52308 228825 4.3746 3.6836
NW_003726423.1 63560 292433 4.6009 4.7272
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NW_003729141.1 4725 24296 5.142 2.7817
NW_003729142.1 4718 20413 4.3266 2.3754
NW_003729143.1 4717 20967 4.445 1.9896
NW_003729144.1 4702 22475 4.7799 1.8985
NW_003729145.1 4702 25009 5.3188 2.6092
NW_003729146.1 4698 23684 5.0413 2.9328
NW_003729147.1 4695 27901 5.9427 2.9022
NW_003729148.1 4694 24295 5.1758 1.948
NW_003729149.1 4689 25794 5.501 2.6993
NW_003729150.1 4688 22940 4.8933 2.7045
NW_003729151.1 4687 22181 4.7325 2.8961
NW_003729152.1 4685 21902 4.6749 2.3609
NW_003729153.1 4683 24600 5.253 2.1013
NW_003729154.1 4681 18604 3.9744 1.9765
NW_003729155.1 4676 23075 4.9348 2.1847
NW_003729156.1 4673 22804 4.8799 2.4544
NW_003729157.1 4673 23099 4.9431 2.3107
NW_003729158.1 4669 23399 5.0116 2.5781
NW_003729159.1 4668 20688 4.4319 2.1516
NW_003729160.1 4662 22791 4.8887 2.1502
NW_003729161.1 4659 27290 5.8575 3.0058
NW_003729162.1 4649 22780 4.9 1.7152
NW_003729163.1 4649 28193 6.0643 2.6186
NW_003729164.1 4639 25787 5.5587 2.6112
NW_003729165.1 4636 20694 4.4638 2.1393
NW_003729166.1 4631 21865 4.7214 2.432
NW_003729167.1 4630 25193 5.4413 2.3348
NW_003729168.1 4629 21607 4.6677 2.4557
NW_003729169.1 4619 23984 5.1925 2.6635
NW_003729170.1 4613 20987 4.5495 2.1427
NW_003729171.1 4612 22792 4.9419 2.5128
NW_003729172.1 4601 23112 5.0233 2.3121
NW_003729173.1 4600 23111 5.0241 2.3207
NW_003729174.1 4600 20091 4.3676 1.9955
NW_003729175.1 4594 25210 5.4876 2.6992
NW_003729176.1 4588 21864 4.7655 2.7727
NW_003729177.1 4580 21584 4.7127 1.8892
NW_003729178.1 4577 21600 4.7192 2.0133
NW_003729179.1 4577 21143 4.6194 2.3797
NW_003729180.1 4577 20705 4.5237 2.4416
NW_003729181.1 4575 24465 5.3475 2.711
NW_003729182.1 4574 23986 5.244 3.0257
NW_003729183.1 4572 21867 4.7828 2.5255
NW_003729184.1 4572 23409 5.1201 2.1065
NW_003729185.1 4562 22794 4.9965 2.4536
NW_003729186.1 4555 23707 5.2046 2.7929
NW_003729187.1 4554 22493 4.9392 2.5037
NW_003729188.1 4552 19804 4.3506 2.546
NW_003729189.1 4550 23406 5.1442 2.2835
NW_003729190.1 4543 23990 5.2807 2.535
NW_003729191.1 4541 22483 4.9511 1.8767
NW_003729192.1 4539 20692 4.5587 2.4513
NW_003729193.1 4527 21002 4.6393 2.5439
NW_003729194.1 4519 22793 5.0438 2.4428
NW_003729195.1 4507 24902 5.5252 2.1998
NW_003729196.1 4501 19472 4.3261 2.6396
NW_003729197.1 4485 22952 5.1175 2.3626
NW_003729198.1 4480 24620 5.4955 2.4296
NW_003729199.1 4476 24586 5.4929 2.3784
NW_003729200.1 4469 19366 4.3334 1.9641
NW_003729201.1 4463 19504 4.3702 2.1094
NW_003729202.1 4460 21001 4.7087 2.0707
NW_003729203.1 4454 20677 4.6423 1.8671
NW_003729204.1 4453 21586 4.8475 2.5442
NW_003729205.1 4447 22490 5.0573 2.6902
NW_003729206.1 4443 23102 5.1996 2.6622
NW_003729207.1 4439 22207 5.0027 2.7975
NW_003729208.1 4437 23985 5.4057 3.4796
NW_003729209.1 4430 18602 4.1991 2.7459
NW_003729210.1 4429 19485 4.3994 2.4789
NW_003729211.1 4428 22190 5.0113 2.5457
NW_003729212.1 4420 22495 5.0894 2.6899
NW_003729213.1 4418 23123 5.2338 2.4951
NW_003729214.1 4418 22187 5.022 2.3244
NW_003729215.1 4408 22827 5.1785 2.7786
NW_003729216.1 4404 19504 4.4287 2.3651
NW_003729217.1 4404 22203 5.0416 2.2588
NW_003729218.1 4403 21895 4.9727 2.6862
NW_003729219.1 4399 20088 4.5665 2.2248
NW_003729220.1 4393 21608 4.9187 2.551
NW_003729221.1 4389 19804 4.5122 2.5054
NW_003729222.1 4389 22051 5.0242 3.412
NW_003729223.1 4388 21124 4.814 2.3884
NW_003729224.1 4378 23083 5.2725 2.0212
NW_003729225.1 4368 23998 5.494 2.5554
NW_003729226.1 4359 21898 5.0236 2.3181
NW_003729227.1 4356 21309 4.8919 2.2193
NW_003729228.1 4353 23113 5.3097 2.5047
NW_003729229.1 4329 19497 4.5038 2.148
NW_003729230.1 4311 25212 5.8483 2.6197
NW_003729231.1 4302 17958 4.1743 2.5282
NW_003729232.1 4300 21319 4.9579 2.5804
NW_003729233.1 4285 22819 5.3253 2.0442
NW_003729234.1 4283 17096 3.9916 2.1931
NW_003729235.1 4282 18594 4.3424 2.1698
NW_003729236.1 4281 22181 5.1813 2.4501
NW_003729237.1 4279 20693 4.8359 2.0772
NW_003729238.1 4277 21285 4.9766 2.5774
NW_003729239.1 4276 21905 5.1228 2.6079
NW_003729240.1 4276 20101 4.7009 2.5513
NW_003729241.1 4252 19491 4.584 2.3364
NW_003729242.1 4248 19797 4.6603 2.0032
NW_003729243.1 4239 20555 4.849 2.754
NW_003729244.1 4238 17695 4.1753 2.469
NW_003729245.1 4234 22207 5.2449 2.5617
NW_003729246.1 4233 19205 4.537 2.9944
NW_003729247.1 4231 17554 4.1489 2.2158
NW_003729248.1 4225 16198 3.8338 1.9434
NW_003729249.1 4201 21600 5.1416 2.0859
NW_003729250.1 4198 19783 4.7125 2.4929
NW_003729251.1 4193 18574 4.4298 2.8409
NW_003729252.1 4186 19953 4.7666 2.3876
NW_003729253.1 4183 21299 5.0918 2.6194
NW_003729254.1 4177 19505 4.6696 2.9871
NW_003729255.1 4172 18284 4.3826 2.5797
NW_003729256.1 4163 18305 4.3971 2.3987
NW_003729257.1 4156 19790 4.7618 2.4487
NW_003729258.1 4141 19761 4.772 3.2309
NW_003729259.1 4130 20704 5.0131 2.5026
NW_003729260.1 4130 19483 4.7174 2.5586
NW_003729261.1 4126 21607 5.2368 2.7604
NW_003729262.1 4123 19209 4.659 2.3425
NW_003729263.1 4121 21282 5.1643 1.8784
NW_003729264.1 4117 19809 4.8115 2.1655
NW_003729265.1 4112 19770 4.8079 2.2554
NW_003729266.1 4097 21754 5.3097 2.3965
NW_003729267.1 4096 20108 4.9092 2.0234
NW_003729268.1 4070 21138 5.1936 2.9977
NW_003729269.1 4064 18577 4.5711 2.7956
NW_003729270.1 4061 17408 4.2866 2.4615
NW_003729271.1 4060 22488 5.5389 2.6748
NW_003729272.1 4025 16650 4.1366 2.3343
NW_003729273.1 4025 18008 4.474 2.2368
NW_003729274.1 4011 20693 5.1591 3.1903
NW_003729275.1 4001 18891 4.7216 2.2389
NW_003729276.1 3976 17843 4.4877 2.5606
NW_003729277.1 3948 19761 5.0053 2.816
NW_003729278.1 3941 18924 4.8018 2.4831
NW_003729279.1 3928 17205 4.3801 1.8292
NW_003729280.1 3925 19186 4.8882 2.4969
NW_003729281.1 3919 17995 4.5917 2.604
NW_003729282.1 3849 16204 4.2099 1.8906
NW_003729283.1 3848 21289 5.5325 2.7361
NW_003729284.1 3847 17694 4.5994 2.8086
NW_003729285.1 3817 18892 4.9494 2.0077
NW_003729286.1 3780 18566 4.9116 2.7855
NW_003729287.1 3780 14410 3.8122 2.1007
NW_003729288.1 3777 17694 4.6847 2.824
NW_003729289.1 3761 17121 4.5522 2.6935
NW_003729290.1 3750 22176 5.9136 2.265
NW_003729291.1 3733 19785 5.3 2.8735
NW_003729292.1 3719 17391 4.6763 2.5407
NW_003729293.1 3718 18040 4.8521 2.7336
NW_003729294.1 3706 16196 4.3702 2.2459
NW_003729295.1 3700 17385 4.6986 2.0958
NW_003729296.1 3695 17392 4.7069 2.7457
NW_003729297.1 3652 19805 5.4231 3.1234
NW_003729298.1 3649 15296 4.1918 1.9062
NW_003729299.1 3629 15019 4.1386 2.5196
NW_003729300.1 3622 18008 4.9718 2.1836
NW_003729301.1 3616 16492 4.5608 2.8783
NW_003729302.1 3614 17092 4.7294 2.1579
NW_003729303.1 3595 17652 4.9102 2.877
NW_003729304.1 3589 18887 5.2625 2.286
NW_003729305.1 3585 20101 5.607 2.3087
NW_003729306.1 3580 16789 4.6897 2.4308
NW_003729307.1 3576 17691 4.9471 2.5015
NW_003729308.1 3564 18286 5.1308 2.7229
NW_003729309.1 3524 16184 4.5925 2.7113
NW_003729310.1 3506 18608 5.3075 2.2182
NW_003729311.1 3484 17369 4.9854 2.0548
NW_003729312.1 3480 16197 4.6543 3.2665
NW_003729313.1 3479 20404 5.8649 2.9213
NW_003729314.1 3440 17119 4.9765 2.5566
NW_003729315.1 3431 18573 5.4133 2.7303
NW_003729316.1 3430 16808 4.9003 2.4655
NW_003729317.1 3407 19799 5.8113 3.3725
NW_003729318.1 3398 18558 5.4614 3.7144
NW_003729319.1 3393 16791 4.9487 2.1569
NW_003729320.1 3388 17530 5.1741 2.4873
NW_003729321.1 3369 13496 4.0059 2.0899
NW_003729322.1 3338 14406 4.3158 2.9983
NW_003729323.1 3331 16194 4.8616 2.3124
NW_003729324.1 3271 16342 4.996 2.3251
NW_003729325.1 3257 13784 4.2321 2.5636
NW_003729326.1 3257 16185 4.9693 2.2827
NW_003729327.1 3231 13201 4.0857 1.9891
NW_003729328.1 3135 18582 5.9273 2.1365
NW_003729329.1 3134 18607 5.9371 2.4059
NW_003729330.1 3059 14985 4.8987 2.8532
NW_003729331.1 3011 15898 5.28 2.8109
NW_003729332.1 2997 16487 5.5012 2.7688
NW_003729333.1 2955 13493 4.5662 2.8535
NW_003729334.1 2933 14394 4.9076 2.7462
NW_003729335.1 2850 15005 5.2649 2.7848
NW_003729336.1 2823 13794 4.8863 1.9779
NW_003729337.1 2809 9887 3.5198 2.3043
NW_003729338.1 2772 12737 4.5949 2.3896
NW_003729339.1 2729 13490 4.9432 2.033
NW_003729340.1 2708 11402 4.2105 2.2367
NW_003729341.1 2700 12304 4.557 2.4012
NW_003729342.1 2641 13174 4.9883 2.4904
NW_003729343.1 2494 11994 4.8091 2.3751
NW_003729344.1 2361 9601 4.0665 1.8516
NW_003729345.1 2327 12001 5.1573 2.9567
NW_003729346.1 2250 11698 5.1991 2.5605
NW_003729347.1 2145 9283 4.3277 1.7371
NW_003729348.1 2046 9894 4.8358 3.6818
NW_003729349.1 1999 11408 5.7069 2.9088
NW_003729350.1 1819 8396 4.6157 2.2546
NW_003729351.1 1790 8094 4.5218 2.5381
NW_003729352.1 1685 8401 4.9858 2.7099
NW_003729353.1 1573 6594 4.192 2.1692
NW_003729354.1 1115 4204 3.7704 2.1946
NC_002008.4 16727 83698 5.0038 2.6794

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 17:54:38
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