Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-219-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-219-TP3_R1_001.fastp-trim.fq.gz -2 POC-219-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-219-TP3 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 02:10:05 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-219-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 54,375,698
Mapped reads 54,375,698 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 54,375,698 / 100%
Mapped reads, first in pair 27,187,849 / 50%
Mapped reads, second in pair 27,187,849 / 50%
Mapped reads, both in pair 54,375,698 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 123.79
Overlapping read pairs 22,537,102 / 82.89%
Duplicated reads (estimated) 9,580,775 / 17.62%
Duplication rate 16.21%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,656,553,967 / 39.63%
Number/percentage of C's 697,923,246 / 10.41%
Number/percentage of T's 2,667,451,937 / 39.79%
Number/percentage of G's 681,506,957 / 10.17%
Number/percentage of N's 600,817 / 0.01%
GC Percentage 20.58%

Coverage

Mean 17.8532
Standard Deviation 24.4252
Mean (paired-end reads overlap ignored) 12.88

Mapping Quality

Mean Mapping Quality 22.66

Insert size

Mean 189.48
Standard Deviation 82.16
P25/Median/P75 135 / 161 / 238

Mismatches and indels

General error rate 22.02%
Mismatches 1,453,226,221
Insertions 9,082,980
Mapped reads with at least one insertion 12.48%
Deletions 7,051,189
Mapped reads with at least one deletion 10.95%
Homopolymer indels 50.48%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 415993740 19.2135 18.0266
Pocillopora_meandrina_HIv1___Sc0000001 21507942 440033693 20.4591 17.8788
Pocillopora_meandrina_HIv1___Sc0000002 19741974 389380978 19.7235 16.5987
Pocillopora_meandrina_HIv1___Sc0000003 19417450 341775541 17.6015 18.7364
Pocillopora_meandrina_HIv1___Sc0000004 14584444 256975600 17.6198 38.5325
Pocillopora_meandrina_HIv1___Sc0000005 14098929 271407456 19.2502 16.2731
Pocillopora_meandrina_HIv1___Sc0000006 14068054 273290524 19.4263 19.5936
Pocillopora_meandrina_HIv1___Sc0000007 13590779 259392433 19.0859 17.8782
Pocillopora_meandrina_HIv1___Sc0000008 12446599 249661055 20.0586 17.5498
Pocillopora_meandrina_HIv1___Sc0000009 11983232 136093060 11.357 35.3177
Pocillopora_meandrina_HIv1___Sc0000010 11763137 209693386 17.8263 19.8078
Pocillopora_meandrina_HIv1___Sc0000011 10501528 234365562 22.3173 16.0224
Pocillopora_meandrina_HIv1___Sc0000012 10024633 189811793 18.9345 30.2866
Pocillopora_meandrina_HIv1___Sc0000013 9946974 133128951 13.3839 16.3602
Pocillopora_meandrina_HIv1___Sc0000014 9536826 193994896 20.3417 16.4601
Pocillopora_meandrina_HIv1___Sc0000015 9393205 176349462 18.7742 17.7366
Pocillopora_meandrina_HIv1___Sc0000016 9288165 162704266 17.5174 16.6531
Pocillopora_meandrina_HIv1___Sc0000017 9274345 168350401 18.1523 16.2449
Pocillopora_meandrina_HIv1___Sc0000018 8584156 166619841 19.4102 16.2788
Pocillopora_meandrina_HIv1___Sc0000019 7112774 131919411 18.5468 19.9509
Pocillopora_meandrina_HIv1___Sc0000020 6748058 133123459 19.7277 20.4646
Pocillopora_meandrina_HIv1___Sc0000021 6546105 134519963 20.5496 17.9146
Pocillopora_meandrina_HIv1___Sc0000022 6319256 107444279 17.0027 23.4371
Pocillopora_meandrina_HIv1___Sc0000023 5767069 79649984 13.8112 15.4319
Pocillopora_meandrina_HIv1___Sc0000024 5762297 65079439 11.294 15.8119
Pocillopora_meandrina_HIv1___Sc0000025 5759531 94535505 16.4138 19.3972
Pocillopora_meandrina_HIv1___Sc0000026 5647578 122723915 21.7304 17.2484
Pocillopora_meandrina_HIv1___Sc0000027 5550630 88746661 15.9886 20.4954
Pocillopora_meandrina_HIv1___Sc0000028 5130920 103321127 20.137 18.0669
Pocillopora_meandrina_HIv1___Sc0000029 4860867 74669952 15.3614 16.3935
Pocillopora_meandrina_HIv1___Sc0000030 4843735 97269001 20.0814 16.2814
Pocillopora_meandrina_HIv1___Sc0000031 4691590 88771065 18.9213 16.1178
Pocillopora_meandrina_HIv1___Sc0000032 3615800 73538458 20.3381 17.3909
Pocillopora_meandrina_HIv1___Sc0000033 3306609 46456637 14.0496 21.779
Pocillopora_meandrina_HIv1___Sc0000034 3122802 61296198 19.6286 17.2987
Pocillopora_meandrina_HIv1___Sc0000035 3015365 41476877 13.7552 16.7015
Pocillopora_meandrina_HIv1___Sc0000036 3007169 66712259 22.1844 17.0818
Pocillopora_meandrina_HIv1___Sc0000037 2860435 53245837 18.6146 19.3839
Pocillopora_meandrina_HIv1___Sc0000038 2701138 44501326 16.475 17.6521
Pocillopora_meandrina_HIv1___Sc0000039 2599273 37442964 14.4052 22.645
Pocillopora_meandrina_HIv1___Sc0000040 2445666 44609783 18.2403 20.1555
Pocillopora_meandrina_HIv1___Sc0000041 2159376 44335140 20.5315 16.6561
Pocillopora_meandrina_HIv1___Sc0000042 1957488 32119649 16.4086 16.657
Pocillopora_meandrina_HIv1___Sc0000043 1845599 32170975 17.4312 16.8129
Pocillopora_meandrina_HIv1___Sc0000044 1724711 34532190 20.022 17.7135
Pocillopora_meandrina_HIv1___Sc0000045 1153740 17625457 15.2768 15.1295
Pocillopora_meandrina_HIv1___Sc0000046 755410 10220283 13.5295 23.3388
Pocillopora_meandrina_HIv1___Sc0000047 239089 169373 0.7084 2.3985
Pocillopora_meandrina_HIv1___Sc0000048 214660 45977 0.2142 1.4885
Pocillopora_meandrina_HIv1___Sc0000049 179266 165982 0.9259 3.4802
Pocillopora_meandrina_HIv1___Sc0000050 177168 283890 1.6024 6.5456
Pocillopora_meandrina_HIv1___Sc0000051 165057 1414023 8.5669 14.9393
Pocillopora_meandrina_HIv1___Sc0000052 155210 74323 0.4789 5.906
Pocillopora_meandrina_HIv1___Sc0000053 123249 307966 2.4987 8.5177
Pocillopora_meandrina_HIv1___Sc0000054 122643 1740358 14.1904 16.9293
Pocillopora_meandrina_HIv1___Sc0000055 121609 803575 6.6079 19.1076
Pocillopora_meandrina_HIv1___Sc0000056 112816 82164 0.7283 9.2731
Pocillopora_meandrina_HIv1___Sc0000057 107171 309159 2.8847 7.2373
Pocillopora_meandrina_HIv1___Sc0000058 98341 44600 0.4535 4.4019
Pocillopora_meandrina_HIv1___Sc0000059 83292 1791 0.0215 0.2418
Pocillopora_meandrina_HIv1___Sc0000060 79483 575 0.0072 0.1169
Pocillopora_meandrina_HIv1___Sc0000061 75390 553628 7.3435 20.4686
Pocillopora_meandrina_HIv1___Sc0000062 74194 20581 0.2774 1.4586
Pocillopora_meandrina_HIv1___Sc0000063 73457 97384 1.3257 14.274
Pocillopora_meandrina_HIv1___Sc0000064 72700 8152 0.1121 0.6339
Pocillopora_meandrina_HIv1___Sc0000065 67986 8447 0.1242 1.4901
Pocillopora_meandrina_HIv1___Sc0000066 66659 438536 6.5788 8.3046
Pocillopora_meandrina_HIv1___Sc0000067 64947 197576 3.0421 7.2791
Pocillopora_meandrina_HIv1___Sc0000068 64340 11280 0.1753 1.3401
Pocillopora_meandrina_HIv1___Sc0000069 62616 224231 3.581 10.3313
Pocillopora_meandrina_HIv1___Sc0000070 60121 131777 2.1919 11.5087
Pocillopora_meandrina_HIv1___Sc0000071 57157 55286 0.9673 3.0412
Pocillopora_meandrina_HIv1___Sc0000072 56626 19424 0.343 4.233
Pocillopora_meandrina_HIv1___Sc0000073 56082 21256 0.379 2.2643
Pocillopora_meandrina_HIv1___Sc0000074 55210 462 0.0084 0.1148
Pocillopora_meandrina_HIv1___Sc0000075 54685 1474 0.027 0.3876
Pocillopora_meandrina_HIv1___Sc0000076 54587 246569 4.517 25.662
Pocillopora_meandrina_HIv1___Sc0000077 53379 18892 0.3539 0.9202
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1336 0.0269 0.2058
Pocillopora_meandrina_HIv1___Sc0000080 47218 157370 3.3328 12.8508
Pocillopora_meandrina_HIv1___Sc0000081 42490 6393 0.1505 0.6462
Pocillopora_meandrina_HIv1___Sc0000082 32657 816934 25.0156 55.8047
Pocillopora_meandrina_HIv1___Sc0000083 27992 4961 0.1772 0.9138
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 19639102 12.2621 21.7297
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 2255144 1.8829 5.6744
Pocillopora_meandrina_HIv1___xfSc0000002 779520 7869961 10.0959 14.9385
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1137688 2.4607 5.5432
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1233190 3.6836 7.0538
Pocillopora_meandrina_HIv1___xfSc0000006 290100 502535 1.7323 4.8144
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1361661 5.3979 9.4635
Pocillopora_meandrina_HIv1___xfSc0000012 148278 659972 4.4509 12.558
Pocillopora_meandrina_HIv1___xfSc0000014 118081 21421 0.1814 0.8536
Pocillopora_meandrina_HIv1___xfSc0000017 98555 930327 9.4397 146.8805
Pocillopora_meandrina_HIv1___xfSc0000021 95778 511824 5.3439 11.5082
Pocillopora_meandrina_HIv1___xfSc0000024 90744 972728 10.7195 20.7317
Pocillopora_meandrina_HIv1___xfSc0000029 85532 514638 6.0169 17.4931
Pocillopora_meandrina_HIv1___xfSc0000038 77395 24453 0.316 2.657
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1383652 19.8464 24.7462
Pocillopora_meandrina_HIv1___xfSc0000059 69426 927741 13.363 10.8634
Pocillopora_meandrina_HIv1___xfSc0000074 66573 226700 3.4053 8.0381
Pocillopora_meandrina_HIv1___xfSc0000081 65415 390116 5.9637 7.9401
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1154414 17.674 25.0816
Pocillopora_meandrina_HIv1___xfSc0000092 63607 852889 13.4087 13.2564
Pocillopora_meandrina_HIv1___xfSc0000094 62842 104286 1.6595 4.2333
Pocillopora_meandrina_HIv1___xfSc0000113 60556 803971 13.2765 15.9716
Pocillopora_meandrina_HIv1___xfSc0000132 59032 86925 1.4725 4.2873
Pocillopora_meandrina_HIv1___xfSc0000145 58221 196771 3.3797 7.3835
Pocillopora_meandrina_HIv1___xfSc0000146 58151 89258 1.5349 4.0323
Pocillopora_meandrina_HIv1___xfSc0000168 56681 359308 6.3391 10.5067
Pocillopora_meandrina_HIv1___xfSc0000175 56271 232712 4.1356 10.4374
Pocillopora_meandrina_HIv1___xfSc0000195 55223 6875 0.1245 1.3279
Pocillopora_meandrina_HIv1___xfSc0000199 55095 451215 8.1898 15.3134
Pocillopora_meandrina_HIv1___xfSc0000205 54658 147152 2.6922 5.2092
Pocillopora_meandrina_HIv1___xfSc0000206 54623 217651 3.9846 6.9529
Pocillopora_meandrina_HIv1___xfSc0000212 54299 407107 7.4975 17.4167
Pocillopora_meandrina_HIv1___xfSc0000217 54168 520463 9.6083 25.4797
Pocillopora_meandrina_HIv1___xfSc0000223 53823 384078 7.1359 9.2079
Pocillopora_meandrina_HIv1___xfSc0000228 53382 498383 9.3362 37.7176
Pocillopora_meandrina_HIv1___xfSc0000237 53049 319635 6.0253 10.0977
Pocillopora_meandrina_HIv1___xfSc0000262 52308 492484 9.4151 11.9278
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1970553 37.7038 39.6689
Pocillopora_meandrina_HIv1___xfSc0000272 52107 544918 10.4577 15.7884
Pocillopora_meandrina_HIv1___xfSc0000275 51938 521725 10.0451 15.099
Pocillopora_meandrina_HIv1___xfSc0000284 51483 333419 6.4763 11.4572
Pocillopora_meandrina_HIv1___xfSc0000288 51367 765445 14.9015 18.9514
Pocillopora_meandrina_HIv1___xfSc0000300 50845 7684 0.1511 0.5433
Pocillopora_meandrina_HIv1___xfSc0000301 50809 550022 10.8253 13.5765
Pocillopora_meandrina_HIv1___xfSc0000343 49544 179462 3.6223 7.0059
Pocillopora_meandrina_HIv1___xfSc0000376 48519 593870 12.2399 39.2425
Pocillopora_meandrina_HIv1___xfSc0000415 47398 232348 4.9021 7.2974
Pocillopora_meandrina_HIv1___xfSc0000423 47202 49530 1.0493 2.8508
Pocillopora_meandrina_HIv1___xfSc0000426 47096 931836 19.7859 25.8998
Pocillopora_meandrina_HIv1___xfSc0000428 47057 282461 6.0025 12.5206
Pocillopora_meandrina_HIv1___xfSc0000436 46816 310878 6.6404 14.542
Pocillopora_meandrina_HIv1___xfSc0000445 46561 101606 2.1822 4.975
Pocillopora_meandrina_HIv1___xfSc0000447 46542 524128 11.2614 14.7685
Pocillopora_meandrina_HIv1___xfSc0000469 45938 414738 9.0282 10.4089
Pocillopora_meandrina_HIv1___xfSc0000477 45781 187604 4.0979 7.1391
Pocillopora_meandrina_HIv1___xfSc0000479 45736 164889 3.6052 6.2862
Pocillopora_meandrina_HIv1___xfSc0000482 45585 507833 11.1404 18.9221
Pocillopora_meandrina_HIv1___xfSc0000488 45379 103166 2.2734 4.6739
Pocillopora_meandrina_HIv1___xfSc0000506 44781 164291 3.6688 6.5974
Pocillopora_meandrina_HIv1___xfSc0000527 44235 257313 5.817 9.342
Pocillopora_meandrina_HIv1___xfSc0000540 43935 333559 7.5921 10.2126
Pocillopora_meandrina_HIv1___xfSc0000555 43535 276855 6.3594 14.0973
Pocillopora_meandrina_HIv1___xfSc0000565 43357 378293 8.7251 10.0756
Pocillopora_meandrina_HIv1___xfSc0000566 43316 271182 6.2606 11.1419
Pocillopora_meandrina_HIv1___xfSc0000567 43305 224857 5.1924 10.8358
Pocillopora_meandrina_HIv1___xfSc0000570 43295 71775 1.6578 4.402
Pocillopora_meandrina_HIv1___xfSc0000579 43029 75801 1.7616 4.8451
Pocillopora_meandrina_HIv1___xfSc0000583 42958 359163 8.3608 9.8581
Pocillopora_meandrina_HIv1___xfSc0000596 42675 201429 4.7201 8.2079
Pocillopora_meandrina_HIv1___xfSc0000612 42423 121621 2.8669 5.2295
Pocillopora_meandrina_HIv1___xfSc0000616 42355 12175418 287.4612 1,209.8277
Pocillopora_meandrina_HIv1___xfSc0000621 42164 534291 12.6717 15.4195
Pocillopora_meandrina_HIv1___xfSc0000642 41754 434622 10.4091 17.8388
Pocillopora_meandrina_HIv1___xfSc0000655 41446 626173 15.1082 32.3314
Pocillopora_meandrina_HIv1___xfSc0000692 40426 71485 1.7683 6.7139
Pocillopora_meandrina_HIv1___xfSc0000699 40296 27387 0.6796 2.5887
Pocillopora_meandrina_HIv1___xfSc0000704 40233 204422 5.081 9.8412
Pocillopora_meandrina_HIv1___xfSc0000705 40197 130460 3.2455 6.7675
Pocillopora_meandrina_HIv1___xfSc0000716 39998 460550 11.5143 13.7159
Pocillopora_meandrina_HIv1___xfSc0000725 39827 62204 1.5619 4.7904
Pocillopora_meandrina_HIv1___xfSc0000729 39775 16379 0.4118 2.221
Pocillopora_meandrina_HIv1___xfSc0000760 39228 6383 0.1627 0.9797
Pocillopora_meandrina_HIv1___xfSc0000763 39151 272172 6.9519 9.0783
Pocillopora_meandrina_HIv1___xfSc0000765 39117 81273 2.0777 6.9584
Pocillopora_meandrina_HIv1___xfSc0000788 38513 349074 9.0638 12.6705
Pocillopora_meandrina_HIv1___xfSc0000811 37888 586623 15.4831 17.1072
Pocillopora_meandrina_HIv1___xfSc0000812 37881 27704 0.7313 3.0762
Pocillopora_meandrina_HIv1___xfSc0000817 37779 480943 12.7304 12.5493
Pocillopora_meandrina_HIv1___xfSc0000824 37656 102336 2.7177 5.1708
Pocillopora_meandrina_HIv1___xfSc0000835 37434 119673 3.1969 6.2426
Pocillopora_meandrina_HIv1___xfSc0000836 37372 289963 7.7588 13.9031
Pocillopora_meandrina_HIv1___xfSc0000837 37368 393117 10.5202 14.4447
Pocillopora_meandrina_HIv1___xfSc0000840 37283 313293 8.4031 14.2563
Pocillopora_meandrina_HIv1___xfSc0000857 37006 191741 5.1813 8.5441
Pocillopora_meandrina_HIv1___xfSc0000859 36995 95522 2.582 5.9146
Pocillopora_meandrina_HIv1___xfSc0000866 36925 64496 1.7467 3.6451
Pocillopora_meandrina_HIv1___xfSc0000868 36831 112464 3.0535 8.2053
Pocillopora_meandrina_HIv1___xfSc0000875 36611 35390 0.9666 3.4298
Pocillopora_meandrina_HIv1___xfSc0000885 36416 198235 5.4436 8.4851
Pocillopora_meandrina_HIv1___xfSc0000886 36355 66465 1.8282 6.3919
Pocillopora_meandrina_HIv1___xfSc0000890 36339 282638 7.7778 15.5862
Pocillopora_meandrina_HIv1___xfSc0000892 36267 78328 2.1598 10.7471
Pocillopora_meandrina_HIv1___xfSc0000943 35168 4496 0.1278 0.6744
Pocillopora_meandrina_HIv1___xfSc0000948 35100 251163 7.1556 11.038
Pocillopora_meandrina_HIv1___xfSc0000952 34934 243902 6.9818 10.3468
Pocillopora_meandrina_HIv1___xfSc0000953 34905 185943 5.3271 8.2964
Pocillopora_meandrina_HIv1___xfSc0000957 34773 139815 4.0208 8.6566
Pocillopora_meandrina_HIv1___xfSc0000968 34345 19718 0.5741 2.5668
Pocillopora_meandrina_HIv1___xfSc0000974 34140 321763 9.4248 11.9095
Pocillopora_meandrina_HIv1___xfSc0000975 33988 617658 18.1728 25.6361
Pocillopora_meandrina_HIv1___xfSc0000995 33324 169028 5.0723 11.8373
Pocillopora_meandrina_HIv1___xfSc0001011 32918 217670 6.6125 12.9537
Pocillopora_meandrina_HIv1___xfSc0001122 29140 321014 11.0163 13.509
Pocillopora_meandrina_HIv1___xfSc0001170 27381 41919 1.531 5.7224
Pocillopora_meandrina_HIv1___xfSc0001179 27200 91307 3.3569 6.5341
Pocillopora_meandrina_HIv1___xfSc0001231 22938 12751 0.5559 1.4109
Pocillopora_meandrina_HIv1___xfSc0001237 22715 34565 1.5217 5.3527
Pocillopora_meandrina_HIv1___xpSc0001273 408270 833027 2.0404 5.7537
Pocillopora_meandrina_HIv1___xpSc0001275 48561 196362 4.0436 8.4803
Pocillopora_meandrina_HIv1___xpSc0001276 38618 40488 1.0484 3.6509
Pocillopora_meandrina_HIv1___xpSc0001280 35955 75823 2.1088 3.9298
Pocillopora_meandrina_HIv1___xpSc0001281 34238 340084 9.9329 37.3203
Pocillopora_meandrina_HIv1___xpSc0001290 28931 201729 6.9728 9.9574
Pocillopora_meandrina_HIv1___xpSc0001321 15304 129558 8.4656 15.3992
Pocillopora_meandrina_HIv1___xpSc0001331 8958 178494 19.9257 12.8059
Pocillopora_meandrina_HIv1___xpSc0001337 6786 23934 3.527 8.0164
Pocillopora_meandrina_HIv1___xpSc0001344 5647 46637 8.2587 11.2739
Pocillopora_meandrina_HIv1___xpSc0001355 3576 73235 20.4796 10.9062

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
    • 2025/04/23 02:10:06
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