Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-259-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-259-TP2_R1_001.fastp-trim.fq.gz -2 POC-259-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-259-TP2 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:44:06 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-259-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 46,172,576
Mapped reads 46,172,576 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 46,172,576 / 100%
Mapped reads, first in pair 23,086,288 / 50%
Mapped reads, second in pair 23,086,288 / 50%
Mapped reads, both in pair 46,172,576 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.26
Overlapping read pairs 11,966,353 / 51.83%
Duplicated reads (estimated) 4,831,615 / 10.46%
Duplication rate 10.21%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,471,885,226 / 40.36%
Number/percentage of C's 593,880,246 / 9.7%
Number/percentage of T's 2,476,709,814 / 40.44%
Number/percentage of G's 581,458,814 / 9.49%
Number/percentage of N's 475,529 / 0.01%
GC Percentage 19.19%

Coverage

Mean 16.3171
Standard Deviation 14.6105
Mean (paired-end reads overlap ignored) 14.33

Mapping Quality

Mean Mapping Quality 22.42

Insert size

Mean 271.9
Standard Deviation 89.76
P25/Median/P75 205 / 264 / 332

Mismatches and indels

General error rate 21.23%
Mismatches 1,275,742,333
Insertions 9,609,887
Mapped reads with at least one insertion 15.45%
Deletions 7,568,499
Mapped reads with at least one deletion 13.66%
Homopolymer indels 51.87%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 377171996 17.4204 12.4378
Pocillopora_meandrina_HIv1___Sc0000001 21507942 391433248 18.1995 11.9727
Pocillopora_meandrina_HIv1___Sc0000002 19741974 349177682 17.6871 12.3264
Pocillopora_meandrina_HIv1___Sc0000003 19417450 298619988 15.3789 13.1669
Pocillopora_meandrina_HIv1___Sc0000004 14584444 235083772 16.1188 26.8599
Pocillopora_meandrina_HIv1___Sc0000005 14098929 244018681 17.3076 13.0705
Pocillopora_meandrina_HIv1___Sc0000006 14068054 242177837 17.2147 12.931
Pocillopora_meandrina_HIv1___Sc0000007 13590779 235811689 17.3509 13.1292
Pocillopora_meandrina_HIv1___Sc0000008 12446599 223802966 17.9811 12.3624
Pocillopora_meandrina_HIv1___Sc0000009 11983232 129196855 10.7815 16.6153
Pocillopora_meandrina_HIv1___Sc0000010 11763137 195019256 16.5788 15.3936
Pocillopora_meandrina_HIv1___Sc0000011 10501528 204044467 19.43 10.8974
Pocillopora_meandrina_HIv1___Sc0000012 10024633 177495472 17.7059 15.0078
Pocillopora_meandrina_HIv1___Sc0000013 9946974 146954509 14.7738 14.5389
Pocillopora_meandrina_HIv1___Sc0000014 9536826 169897089 17.8148 11.8926
Pocillopora_meandrina_HIv1___Sc0000015 9393205 152074157 16.1898 11.6939
Pocillopora_meandrina_HIv1___Sc0000016 9288165 152431734 16.4114 12.4689
Pocillopora_meandrina_HIv1___Sc0000017 9274345 152433565 16.436 11.7597
Pocillopora_meandrina_HIv1___Sc0000018 8584156 146459189 17.0616 11.4273
Pocillopora_meandrina_HIv1___Sc0000019 7112774 115834853 16.2855 12.746
Pocillopora_meandrina_HIv1___Sc0000020 6748058 120137361 17.8032 16.3325
Pocillopora_meandrina_HIv1___Sc0000021 6546105 116243317 17.7576 12.1629
Pocillopora_meandrina_HIv1___Sc0000022 6319256 100233194 15.8615 15.889
Pocillopora_meandrina_HIv1___Sc0000023 5767069 78229929 13.5649 12.222
Pocillopora_meandrina_HIv1___Sc0000024 5762297 64186746 11.1391 13.4362
Pocillopora_meandrina_HIv1___Sc0000025 5759531 80623835 13.9983 13.1807
Pocillopora_meandrina_HIv1___Sc0000026 5647578 113606296 20.1159 12.876
Pocillopora_meandrina_HIv1___Sc0000027 5550630 102500357 18.4664 23.0074
Pocillopora_meandrina_HIv1___Sc0000028 5130920 100776856 19.6411 16.5641
Pocillopora_meandrina_HIv1___Sc0000029 4860867 73465222 15.1136 13.3464
Pocillopora_meandrina_HIv1___Sc0000030 4843735 84106355 17.3639 10.6556
Pocillopora_meandrina_HIv1___Sc0000031 4691590 79497515 16.9447 11.55
Pocillopora_meandrina_HIv1___Sc0000032 3615800 68625288 18.9793 13.2381
Pocillopora_meandrina_HIv1___Sc0000033 3306609 42654430 12.8998 12.6947
Pocillopora_meandrina_HIv1___Sc0000034 3122802 58783313 18.8239 12.9633
Pocillopora_meandrina_HIv1___Sc0000035 3015365 43892660 14.5563 15.5303
Pocillopora_meandrina_HIv1___Sc0000036 3007169 58334782 19.3986 10.8422
Pocillopora_meandrina_HIv1___Sc0000037 2860435 49709563 17.3783 13.1363
Pocillopora_meandrina_HIv1___Sc0000038 2701138 44784454 16.5798 14.8042
Pocillopora_meandrina_HIv1___Sc0000039 2599273 32776091 12.6097 14.0815
Pocillopora_meandrina_HIv1___Sc0000040 2445666 38485891 15.7364 13.2977
Pocillopora_meandrina_HIv1___Sc0000041 2159376 39341922 18.2191 12.4325
Pocillopora_meandrina_HIv1___Sc0000042 1957488 28318924 14.467 12.2544
Pocillopora_meandrina_HIv1___Sc0000043 1845599 27668311 14.9915 12.2139
Pocillopora_meandrina_HIv1___Sc0000044 1724711 30839429 17.8809 12.4364
Pocillopora_meandrina_HIv1___Sc0000045 1153740 15539271 13.4686 12.3416
Pocillopora_meandrina_HIv1___Sc0000046 755410 9196789 12.1746 15.6156
Pocillopora_meandrina_HIv1___Sc0000047 239089 2423176 10.135 13.1446
Pocillopora_meandrina_HIv1___Sc0000048 214660 96996 0.4519 2.6128
Pocillopora_meandrina_HIv1___Sc0000049 179266 453273 2.5285 6.9477
Pocillopora_meandrina_HIv1___Sc0000050 177168 278317 1.5709 4.3863
Pocillopora_meandrina_HIv1___Sc0000051 165057 1553858 9.4141 12.3246
Pocillopora_meandrina_HIv1___Sc0000052 155210 7186 0.0463 0.2944
Pocillopora_meandrina_HIv1___Sc0000053 123249 257786 2.0916 4.7256
Pocillopora_meandrina_HIv1___Sc0000054 122643 2084509 16.9966 15.6555
Pocillopora_meandrina_HIv1___Sc0000055 121609 677428 5.5705 9.6575
Pocillopora_meandrina_HIv1___Sc0000056 112816 77245 0.6847 6.7477
Pocillopora_meandrina_HIv1___Sc0000057 107171 1187861 11.0838 25.9314
Pocillopora_meandrina_HIv1___Sc0000058 98341 9355 0.0951 1.2461
Pocillopora_meandrina_HIv1___Sc0000059 83292 14438 0.1733 0.6891
Pocillopora_meandrina_HIv1___Sc0000060 79483 1097 0.0138 0.1257
Pocillopora_meandrina_HIv1___Sc0000061 75390 239269 3.1737 6.4476
Pocillopora_meandrina_HIv1___Sc0000062 74194 22876 0.3083 1.2837
Pocillopora_meandrina_HIv1___Sc0000063 73457 59484 0.8098 8.8768
Pocillopora_meandrina_HIv1___Sc0000064 72700 6200 0.0853 0.3743
Pocillopora_meandrina_HIv1___Sc0000065 67986 5575 0.082 0.4665
Pocillopora_meandrina_HIv1___Sc0000066 66659 478602 7.1799 7.3788
Pocillopora_meandrina_HIv1___Sc0000067 64947 200472 3.0867 5.5861
Pocillopora_meandrina_HIv1___Sc0000068 64340 43359 0.6739 2.0265
Pocillopora_meandrina_HIv1___Sc0000069 62616 492942 7.8725 8.5582
Pocillopora_meandrina_HIv1___Sc0000070 60121 285404 4.7472 23.7955
Pocillopora_meandrina_HIv1___Sc0000071 57157 83507 1.461 2.8103
Pocillopora_meandrina_HIv1___Sc0000072 56626 14539 0.2568 2.3992
Pocillopora_meandrina_HIv1___Sc0000073 56082 13180 0.235 0.6406
Pocillopora_meandrina_HIv1___Sc0000074 55210 1336 0.0242 0.2108
Pocillopora_meandrina_HIv1___Sc0000075 54685 4625 0.0846 0.3756
Pocillopora_meandrina_HIv1___Sc0000076 54587 201083 3.6837 18.277
Pocillopora_meandrina_HIv1___Sc0000077 53379 32002 0.5995 1.0407
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 3133 0.0631 0.2963
Pocillopora_meandrina_HIv1___Sc0000080 47218 113187 2.3971 5.6811
Pocillopora_meandrina_HIv1___Sc0000081 42490 9671 0.2276 0.5845
Pocillopora_meandrina_HIv1___Sc0000082 32657 1214848 37.2002 64.4943
Pocillopora_meandrina_HIv1___Sc0000083 27992 142549 5.0925 2.8229
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 17347866 10.8315 16.6034
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 7848546 6.5529 9.7408
Pocillopora_meandrina_HIv1___xfSc0000002 779520 6453969 8.2794 11.7318
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2009920 4.3472 6.4585
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1504723 4.4947 7.2248
Pocillopora_meandrina_HIv1___xfSc0000006 290100 597662 2.0602 4.3293
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1468202 5.8202 7.5737
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1633405 11.0158 10.8967
Pocillopora_meandrina_HIv1___xfSc0000014 118081 31382 0.2658 0.9687
Pocillopora_meandrina_HIv1___xfSc0000017 98555 347344 3.5244 34.7325
Pocillopora_meandrina_HIv1___xfSc0000021 95778 701007 7.3191 13.7698
Pocillopora_meandrina_HIv1___xfSc0000024 90744 585354 6.4506 9.517
Pocillopora_meandrina_HIv1___xfSc0000029 85532 170814 1.9971 7.2883
Pocillopora_meandrina_HIv1___xfSc0000038 77395 25538 0.33 1.8911
Pocillopora_meandrina_HIv1___xfSc0000058 69718 655740 9.4056 12.2516
Pocillopora_meandrina_HIv1___xfSc0000059 69426 848858 12.2268 13.4992
Pocillopora_meandrina_HIv1___xfSc0000074 66573 335021 5.0324 6.5607
Pocillopora_meandrina_HIv1___xfSc0000081 65415 651008 9.952 6.8775
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1653914 25.3213 16.8253
Pocillopora_meandrina_HIv1___xfSc0000092 63607 615758 9.6807 8.1272
Pocillopora_meandrina_HIv1___xfSc0000094 62842 326291 5.1922 10.8373
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1142743 18.8708 16.3152
Pocillopora_meandrina_HIv1___xfSc0000132 59032 895584 15.1712 19.0471
Pocillopora_meandrina_HIv1___xfSc0000145 58221 295002 5.0669 6.0688
Pocillopora_meandrina_HIv1___xfSc0000146 58151 540877 9.3013 9.9939
Pocillopora_meandrina_HIv1___xfSc0000168 56681 475007 8.3804 8.849
Pocillopora_meandrina_HIv1___xfSc0000175 56271 371991 6.6107 14.6324
Pocillopora_meandrina_HIv1___xfSc0000195 55223 151359 2.7409 5.1218
Pocillopora_meandrina_HIv1___xfSc0000199 55095 359348 6.5223 10.9368
Pocillopora_meandrina_HIv1___xfSc0000205 54658 974123 17.8221 21.4973
Pocillopora_meandrina_HIv1___xfSc0000206 54623 378625 6.9316 11.3543
Pocillopora_meandrina_HIv1___xfSc0000212 54299 417343 7.686 11.1065
Pocillopora_meandrina_HIv1___xfSc0000217 54168 395054 7.2931 14.3103
Pocillopora_meandrina_HIv1___xfSc0000223 53823 356703 6.6273 7.5183
Pocillopora_meandrina_HIv1___xfSc0000228 53382 347106 6.5023 20.3672
Pocillopora_meandrina_HIv1___xfSc0000237 53049 419597 7.9096 7.903
Pocillopora_meandrina_HIv1___xfSc0000262 52308 388615 7.4294 7.7803
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2659192 50.88 82.1268
Pocillopora_meandrina_HIv1___xfSc0000272 52107 746293 14.3223 16.3073
Pocillopora_meandrina_HIv1___xfSc0000275 51938 638438 12.2923 11.3047
Pocillopora_meandrina_HIv1___xfSc0000284 51483 585007 11.3631 12.3473
Pocillopora_meandrina_HIv1___xfSc0000288 51367 445749 8.6777 13.9111
Pocillopora_meandrina_HIv1___xfSc0000300 50845 13846 0.2723 0.7884
Pocillopora_meandrina_HIv1___xfSc0000301 50809 711748 14.0083 13.5689
Pocillopora_meandrina_HIv1___xfSc0000343 49544 397078 8.0147 11.6234
Pocillopora_meandrina_HIv1___xfSc0000376 48519 410024 8.4508 20.3613
Pocillopora_meandrina_HIv1___xfSc0000415 47398 304000 6.4138 7.6593
Pocillopora_meandrina_HIv1___xfSc0000423 47202 106506 2.2564 5.093
Pocillopora_meandrina_HIv1___xfSc0000426 47096 3099537 65.8132 65.0529
Pocillopora_meandrina_HIv1___xfSc0000428 47057 321661 6.8356 12.2915
Pocillopora_meandrina_HIv1___xfSc0000436 46816 517711 11.0584 17.194
Pocillopora_meandrina_HIv1___xfSc0000445 46561 664480 14.2712 11.7966
Pocillopora_meandrina_HIv1___xfSc0000447 46542 639423 13.7386 12.7394
Pocillopora_meandrina_HIv1___xfSc0000469 45938 523765 11.4016 7.2897
Pocillopora_meandrina_HIv1___xfSc0000477 45781 242440 5.2956 6.7155
Pocillopora_meandrina_HIv1___xfSc0000479 45736 170103 3.7192 5.7297
Pocillopora_meandrina_HIv1___xfSc0000482 45585 607561 13.3281 19.385
Pocillopora_meandrina_HIv1___xfSc0000488 45379 245119 5.4016 8.0372
Pocillopora_meandrina_HIv1___xfSc0000506 44781 421559 9.4138 11.7247
Pocillopora_meandrina_HIv1___xfSc0000527 44235 336517 7.6075 8.2633
Pocillopora_meandrina_HIv1___xfSc0000540 43935 370665 8.4367 11.2157
Pocillopora_meandrina_HIv1___xfSc0000555 43535 351612 8.0765 12.352
Pocillopora_meandrina_HIv1___xfSc0000565 43357 291690 6.7276 6.5594
Pocillopora_meandrina_HIv1___xfSc0000566 43316 266758 6.1584 6.6761
Pocillopora_meandrina_HIv1___xfSc0000567 43305 182006 4.2029 7.0179
Pocillopora_meandrina_HIv1___xfSc0000570 43295 219156 5.0619 7.0627
Pocillopora_meandrina_HIv1___xfSc0000579 43029 102478 2.3816 4.3988
Pocillopora_meandrina_HIv1___xfSc0000583 42958 334788 7.7934 8.8389
Pocillopora_meandrina_HIv1___xfSc0000596 42675 240561 5.637 9.6713
Pocillopora_meandrina_HIv1___xfSc0000612 42423 226994 5.3507 5.1152
Pocillopora_meandrina_HIv1___xfSc0000616 42355 3114883 73.5423 217.0908
Pocillopora_meandrina_HIv1___xfSc0000621 42164 204030 4.839 6.2162
Pocillopora_meandrina_HIv1___xfSc0000642 41754 180848 4.3313 8.6612
Pocillopora_meandrina_HIv1___xfSc0000655 41446 178485 4.3064 7.7833
Pocillopora_meandrina_HIv1___xfSc0000692 40426 59939 1.4827 4.1596
Pocillopora_meandrina_HIv1___xfSc0000699 40296 75603 1.8762 3.6177
Pocillopora_meandrina_HIv1___xfSc0000704 40233 406373 10.1005 13.1137
Pocillopora_meandrina_HIv1___xfSc0000705 40197 180720 4.4959 5.571
Pocillopora_meandrina_HIv1___xfSc0000716 39998 390963 9.7746 10.306
Pocillopora_meandrina_HIv1___xfSc0000725 39827 325106 8.163 17.4952
Pocillopora_meandrina_HIv1___xfSc0000729 39775 23593 0.5932 3.6584
Pocillopora_meandrina_HIv1___xfSc0000760 39228 32804 0.8362 2.3533
Pocillopora_meandrina_HIv1___xfSc0000763 39151 430317 10.9912 6.7211
Pocillopora_meandrina_HIv1___xfSc0000765 39117 210222 5.3742 8.9559
Pocillopora_meandrina_HIv1___xfSc0000788 38513 548080 14.231 13.0809
Pocillopora_meandrina_HIv1___xfSc0000811 37888 312755 8.2547 6.7474
Pocillopora_meandrina_HIv1___xfSc0000812 37881 18666 0.4928 0.9486
Pocillopora_meandrina_HIv1___xfSc0000817 37779 619863 16.4076 10.2458
Pocillopora_meandrina_HIv1___xfSc0000824 37656 144033 3.825 6.0901
Pocillopora_meandrina_HIv1___xfSc0000835 37434 433770 11.5876 11.774
Pocillopora_meandrina_HIv1___xfSc0000836 37372 187227 5.0098 8.2618
Pocillopora_meandrina_HIv1___xfSc0000837 37368 213298 5.708 10.5672
Pocillopora_meandrina_HIv1___xfSc0000840 37283 294846 7.9083 12.1921
Pocillopora_meandrina_HIv1___xfSc0000857 37006 199137 5.3812 9.0329
Pocillopora_meandrina_HIv1___xfSc0000859 36995 95161 2.5723 6.8953
Pocillopora_meandrina_HIv1___xfSc0000866 36925 129315 3.5021 5.5821
Pocillopora_meandrina_HIv1___xfSc0000868 36831 230384 6.2552 11.7436
Pocillopora_meandrina_HIv1___xfSc0000875 36611 63314 1.7294 3.5072
Pocillopora_meandrina_HIv1___xfSc0000885 36416 289799 7.958 10.1402
Pocillopora_meandrina_HIv1___xfSc0000886 36355 153201 4.214 6.851
Pocillopora_meandrina_HIv1___xfSc0000890 36339 248103 6.8275 7.9033
Pocillopora_meandrina_HIv1___xfSc0000892 36267 158182 4.3616 20.0862
Pocillopora_meandrina_HIv1___xfSc0000943 35168 17907 0.5092 2.1242
Pocillopora_meandrina_HIv1___xfSc0000948 35100 369075 10.515 12.0438
Pocillopora_meandrina_HIv1___xfSc0000952 34934 369530 10.5779 6.9919
Pocillopora_meandrina_HIv1___xfSc0000953 34905 175542 5.0291 5.8903
Pocillopora_meandrina_HIv1___xfSc0000957 34773 193946 5.5775 10.2587
Pocillopora_meandrina_HIv1___xfSc0000968 34345 51378 1.4959 4.112
Pocillopora_meandrina_HIv1___xfSc0000974 34140 352430 10.3231 8.3422
Pocillopora_meandrina_HIv1___xfSc0000975 33988 328212 9.6567 8.9917
Pocillopora_meandrina_HIv1___xfSc0000995 33324 132547 3.9775 8.7818
Pocillopora_meandrina_HIv1___xfSc0001011 32918 302432 9.1874 10.9258
Pocillopora_meandrina_HIv1___xfSc0001122 29140 354092 12.1514 11.2893
Pocillopora_meandrina_HIv1___xfSc0001170 27381 50221 1.8342 3.1202
Pocillopora_meandrina_HIv1___xfSc0001179 27200 109146 4.0127 5.9479
Pocillopora_meandrina_HIv1___xfSc0001231 22938 29176 1.272 1.8955
Pocillopora_meandrina_HIv1___xfSc0001237 22715 136580 6.0128 13.6647
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3266191 8.0001 10.8776
Pocillopora_meandrina_HIv1___xpSc0001275 48561 193332 3.9812 7.6321
Pocillopora_meandrina_HIv1___xpSc0001276 38618 146938 3.8049 8.8803
Pocillopora_meandrina_HIv1___xpSc0001280 35955 279616 7.7768 12.2278
Pocillopora_meandrina_HIv1___xpSc0001281 34238 326068 9.5236 12.3205
Pocillopora_meandrina_HIv1___xpSc0001290 28931 1342045 46.3878 27.3344
Pocillopora_meandrina_HIv1___xpSc0001321 15304 57262 3.7416 7.4239
Pocillopora_meandrina_HIv1___xpSc0001331 8958 181575 20.2696 12.6022
Pocillopora_meandrina_HIv1___xpSc0001337 6786 84264 12.4173 6.8354
Pocillopora_meandrina_HIv1___xpSc0001344 5647 52035 9.2146 11.4862
Pocillopora_meandrina_HIv1___xpSc0001355 3576 25439 7.1138 6.4191

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

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
  • Homopolymer Indels
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2025/04/22 21:44:11
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