Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-259-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-259-TP1_R1_001.fastp-trim.fq.gz -2 POC-259-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-259-TP1 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:12:02 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-259-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 48,632,102
Mapped reads 48,632,102 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 48,632,102 / 100%
Mapped reads, first in pair 24,316,051 / 50%
Mapped reads, second in pair 24,316,051 / 50%
Mapped reads, both in pair 48,632,102 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.52
Overlapping read pairs 14,808,518 / 60.9%
Duplicated reads (estimated) 5,546,627 / 11.41%
Duplication rate 11.13%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,582,554,770 / 40.26%
Number/percentage of C's 629,930,562 / 9.82%
Number/percentage of T's 2,584,501,386 / 40.29%
Number/percentage of G's 617,476,296 / 9.63%
Number/percentage of N's 536,671 / 0.01%
GC Percentage 19.45%

Coverage

Mean 17.0891
Standard Deviation 15.9627
Mean (paired-end reads overlap ignored) 14.51

Mapping Quality

Mean Mapping Quality 22.56

Insert size

Mean 251.91
Standard Deviation 85.26
P25/Median/P75 188 / 244 / 306

Mismatches and indels

General error rate 21.14%
Mismatches 1,331,181,518
Insertions 9,772,822
Mapped reads with at least one insertion 14.83%
Deletions 7,553,212
Mapped reads with at least one deletion 13.02%
Homopolymer indels 52.03%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 400010874 18.4753 13.0951
Pocillopora_meandrina_HIv1___Sc0000001 21507942 413829051 19.2408 12.7749
Pocillopora_meandrina_HIv1___Sc0000002 19741974 369837516 18.7336 12.9765
Pocillopora_meandrina_HIv1___Sc0000003 19417450 314450797 16.1942 13.9677
Pocillopora_meandrina_HIv1___Sc0000004 14584444 242039893 16.5958 26.2713
Pocillopora_meandrina_HIv1___Sc0000005 14098929 262337607 18.6069 13.9574
Pocillopora_meandrina_HIv1___Sc0000006 14068054 257750886 18.3217 13.9153
Pocillopora_meandrina_HIv1___Sc0000007 13590779 246144968 18.1112 13.8252
Pocillopora_meandrina_HIv1___Sc0000008 12446599 240729812 19.341 13.1407
Pocillopora_meandrina_HIv1___Sc0000009 11983232 126695112 10.5727 17.1611
Pocillopora_meandrina_HIv1___Sc0000010 11763137 204055785 17.3471 16.644
Pocillopora_meandrina_HIv1___Sc0000011 10501528 219064988 20.8603 11.5233
Pocillopora_meandrina_HIv1___Sc0000012 10024633 182174638 18.1727 16.4111
Pocillopora_meandrina_HIv1___Sc0000013 9946974 143677021 14.4443 14.7066
Pocillopora_meandrina_HIv1___Sc0000014 9536826 181780965 19.061 12.5205
Pocillopora_meandrina_HIv1___Sc0000015 9393205 163500059 17.4062 12.619
Pocillopora_meandrina_HIv1___Sc0000016 9288165 158646919 17.0805 12.8947
Pocillopora_meandrina_HIv1___Sc0000017 9274345 160769387 17.3349 12.5434
Pocillopora_meandrina_HIv1___Sc0000018 8584156 155881050 18.1592 12.2822
Pocillopora_meandrina_HIv1___Sc0000019 7112774 122214867 17.1824 13.5691
Pocillopora_meandrina_HIv1___Sc0000020 6748058 124897402 18.5086 16.928
Pocillopora_meandrina_HIv1___Sc0000021 6546105 125037765 19.1011 13.0725
Pocillopora_meandrina_HIv1___Sc0000022 6319256 101798695 16.1093 16.9484
Pocillopora_meandrina_HIv1___Sc0000023 5767069 83028340 14.397 13.0278
Pocillopora_meandrina_HIv1___Sc0000024 5762297 65074181 11.2931 14.3092
Pocillopora_meandrina_HIv1___Sc0000025 5759531 84306861 14.6378 14.1727
Pocillopora_meandrina_HIv1___Sc0000026 5647578 121101123 21.443 15.4018
Pocillopora_meandrina_HIv1___Sc0000027 5550630 105694481 19.0419 23.6643
Pocillopora_meandrina_HIv1___Sc0000028 5130920 105510179 20.5636 17.2752
Pocillopora_meandrina_HIv1___Sc0000029 4860867 80222210 16.5037 15.543
Pocillopora_meandrina_HIv1___Sc0000030 4843735 90670067 18.719 12.0945
Pocillopora_meandrina_HIv1___Sc0000031 4691590 84521781 18.0156 12.0897
Pocillopora_meandrina_HIv1___Sc0000032 3615800 72709737 20.1089 13.7415
Pocillopora_meandrina_HIv1___Sc0000033 3306609 44636708 13.4992 14.0824
Pocillopora_meandrina_HIv1___Sc0000034 3122802 60038177 19.2257 13.4545
Pocillopora_meandrina_HIv1___Sc0000035 3015365 44973696 14.9148 16.4043
Pocillopora_meandrina_HIv1___Sc0000036 3007169 62359888 20.7371 11.4489
Pocillopora_meandrina_HIv1___Sc0000037 2860435 52717379 18.4298 15.6243
Pocillopora_meandrina_HIv1___Sc0000038 2701138 46993543 17.3977 15.7159
Pocillopora_meandrina_HIv1___Sc0000039 2599273 34795567 13.3867 23.7286
Pocillopora_meandrina_HIv1___Sc0000040 2445666 40627762 16.6121 14.1741
Pocillopora_meandrina_HIv1___Sc0000041 2159376 41439512 19.1905 12.8299
Pocillopora_meandrina_HIv1___Sc0000042 1957488 30059679 15.3563 13.0683
Pocillopora_meandrina_HIv1___Sc0000043 1845599 28884405 15.6504 13.0672
Pocillopora_meandrina_HIv1___Sc0000044 1724711 32115527 18.6208 12.7451
Pocillopora_meandrina_HIv1___Sc0000045 1153740 16473340 14.2782 13.3585
Pocillopora_meandrina_HIv1___Sc0000046 755410 9297242 12.3075 18.1192
Pocillopora_meandrina_HIv1___Sc0000047 239089 343987 1.4387 4.7648
Pocillopora_meandrina_HIv1___Sc0000048 214660 53397 0.2488 1.6579
Pocillopora_meandrina_HIv1___Sc0000049 179266 430533 2.4016 6.2743
Pocillopora_meandrina_HIv1___Sc0000050 177168 217905 1.2299 3.8874
Pocillopora_meandrina_HIv1___Sc0000051 165057 1293079 7.8341 12.0707
Pocillopora_meandrina_HIv1___Sc0000052 155210 12363 0.0797 0.9759
Pocillopora_meandrina_HIv1___Sc0000053 123249 190468 1.5454 3.7552
Pocillopora_meandrina_HIv1___Sc0000054 122643 1598477 13.0336 13.5957
Pocillopora_meandrina_HIv1___Sc0000055 121609 552467 4.543 9.7327
Pocillopora_meandrina_HIv1___Sc0000056 112816 93778 0.8312 7.6932
Pocillopora_meandrina_HIv1___Sc0000057 107171 1132204 10.5645 26.1192
Pocillopora_meandrina_HIv1___Sc0000058 98341 13390 0.1362 1.4837
Pocillopora_meandrina_HIv1___Sc0000059 83292 4245 0.051 0.4308
Pocillopora_meandrina_HIv1___Sc0000060 79483 263 0.0033 0.0567
Pocillopora_meandrina_HIv1___Sc0000061 75390 291279 3.8636 8.6275
Pocillopora_meandrina_HIv1___Sc0000062 74194 25679 0.3461 1.4851
Pocillopora_meandrina_HIv1___Sc0000063 73457 67290 0.916 9.3416
Pocillopora_meandrina_HIv1___Sc0000064 72700 8230 0.1132 0.5074
Pocillopora_meandrina_HIv1___Sc0000065 67986 7863 0.1157 0.6177
Pocillopora_meandrina_HIv1___Sc0000066 66659 527586 7.9147 8.3823
Pocillopora_meandrina_HIv1___Sc0000067 64947 151324 2.33 4.7679
Pocillopora_meandrina_HIv1___Sc0000068 64340 9981 0.1551 0.9579
Pocillopora_meandrina_HIv1___Sc0000069 62616 204201 3.2612 8.3955
Pocillopora_meandrina_HIv1___Sc0000070 60121 331988 5.522 29.9171
Pocillopora_meandrina_HIv1___Sc0000071 57157 80021 1.4 3.0169
Pocillopora_meandrina_HIv1___Sc0000072 56626 15851 0.2799 3.1716
Pocillopora_meandrina_HIv1___Sc0000073 56082 11729 0.2091 0.6924
Pocillopora_meandrina_HIv1___Sc0000074 55210 244 0.0044 0.0695
Pocillopora_meandrina_HIv1___Sc0000075 54685 806 0.0147 0.194
Pocillopora_meandrina_HIv1___Sc0000076 54587 230866 4.2293 20.8608
Pocillopora_meandrina_HIv1___Sc0000077 53379 27416 0.5136 1.1407
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 733 0.0148 0.1524
Pocillopora_meandrina_HIv1___Sc0000080 47218 101131 2.1418 5.8581
Pocillopora_meandrina_HIv1___Sc0000081 42490 10101 0.2377 0.7679
Pocillopora_meandrina_HIv1___Sc0000082 32657 1033293 31.6408 71.9191
Pocillopora_meandrina_HIv1___Sc0000083 27992 4650 0.1661 0.8801
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 15034925 9.3874 15.44
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4264017 3.5601 6.9719
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5383087 6.9056 10.5003
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1302683 2.8175 5.5055
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1317213 3.9346 6.4845
Pocillopora_meandrina_HIv1___xfSc0000006 290100 528960 1.8234 4.5627
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1501469 5.9521 8.1688
Pocillopora_meandrina_HIv1___xfSc0000012 148278 715128 4.8229 8.3773
Pocillopora_meandrina_HIv1___xfSc0000014 118081 33616 0.2847 1.005
Pocillopora_meandrina_HIv1___xfSc0000017 98555 442960 4.4945 50.6431
Pocillopora_meandrina_HIv1___xfSc0000021 95778 694506 7.2512 14.7479
Pocillopora_meandrina_HIv1___xfSc0000024 90744 599705 6.6088 10.6427
Pocillopora_meandrina_HIv1___xfSc0000029 85532 158408 1.852 7.4147
Pocillopora_meandrina_HIv1___xfSc0000038 77395 24912 0.3219 1.9933
Pocillopora_meandrina_HIv1___xfSc0000058 69718 680379 9.759 13.1323
Pocillopora_meandrina_HIv1___xfSc0000059 69426 663923 9.563 10.9339
Pocillopora_meandrina_HIv1___xfSc0000074 66573 169460 2.5455 5.5827
Pocillopora_meandrina_HIv1___xfSc0000081 65415 406469 6.2137 7.1744
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1295225 19.8298 17.1549
Pocillopora_meandrina_HIv1___xfSc0000092 63607 492335 7.7403 8.9051
Pocillopora_meandrina_HIv1___xfSc0000094 62842 127827 2.0341 4.5608
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1069648 17.6638 19.6177
Pocillopora_meandrina_HIv1___xfSc0000132 59032 43979 0.745 2.0705
Pocillopora_meandrina_HIv1___xfSc0000145 58221 225664 3.876 6.4289
Pocillopora_meandrina_HIv1___xfSc0000146 58151 163922 2.8189 6.9911
Pocillopora_meandrina_HIv1___xfSc0000168 56681 329206 5.808 8.6626
Pocillopora_meandrina_HIv1___xfSc0000175 56271 301671 5.361 13.9196
Pocillopora_meandrina_HIv1___xfSc0000195 55223 11075 0.2006 1.4553
Pocillopora_meandrina_HIv1___xfSc0000199 55095 385728 7.0011 11.1128
Pocillopora_meandrina_HIv1___xfSc0000205 54658 665319 12.1724 22.5403
Pocillopora_meandrina_HIv1___xfSc0000206 54623 285741 5.2311 7.7573
Pocillopora_meandrina_HIv1___xfSc0000212 54299 397702 7.3243 10.6849
Pocillopora_meandrina_HIv1___xfSc0000217 54168 342685 6.3263 13.5137
Pocillopora_meandrina_HIv1___xfSc0000223 53823 395863 7.3549 8.1635
Pocillopora_meandrina_HIv1___xfSc0000228 53382 347583 6.5112 22.8142
Pocillopora_meandrina_HIv1___xfSc0000237 53049 303956 5.7297 8.283
Pocillopora_meandrina_HIv1___xfSc0000262 52308 420126 8.0318 7.9243
Pocillopora_meandrina_HIv1___xfSc0000264 52264 872244 16.6892 20.9081
Pocillopora_meandrina_HIv1___xfSc0000272 52107 625544 12.005 16.0536
Pocillopora_meandrina_HIv1___xfSc0000275 51938 561991 10.8204 12.1573
Pocillopora_meandrina_HIv1___xfSc0000284 51483 530930 10.3127 12.6419
Pocillopora_meandrina_HIv1___xfSc0000288 51367 213971 4.1655 12.0148
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9234 0.1816 0.5818
Pocillopora_meandrina_HIv1___xfSc0000301 50809 754170 14.8432 14.589
Pocillopora_meandrina_HIv1___xfSc0000343 49544 341362 6.8901 9.6976
Pocillopora_meandrina_HIv1___xfSc0000376 48519 384395 7.9226 22.9142
Pocillopora_meandrina_HIv1___xfSc0000415 47398 221031 4.6633 5.9753
Pocillopora_meandrina_HIv1___xfSc0000423 47202 59954 1.2702 3.7434
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1907230 40.4966 55.4147
Pocillopora_meandrina_HIv1___xfSc0000428 47057 345227 7.3364 14.0155
Pocillopora_meandrina_HIv1___xfSc0000436 46816 399354 8.5303 17.6673
Pocillopora_meandrina_HIv1___xfSc0000445 46561 168509 3.6191 6.731
Pocillopora_meandrina_HIv1___xfSc0000447 46542 483827 10.3955 12.9491
Pocillopora_meandrina_HIv1___xfSc0000469 45938 432410 9.4129 8.4353
Pocillopora_meandrina_HIv1___xfSc0000477 45781 261807 5.7187 7.7137
Pocillopora_meandrina_HIv1___xfSc0000479 45736 174221 3.8093 6.5009
Pocillopora_meandrina_HIv1___xfSc0000482 45585 306220 6.7176 12.4578
Pocillopora_meandrina_HIv1___xfSc0000488 45379 238844 5.2633 8.3641
Pocillopora_meandrina_HIv1___xfSc0000506 44781 167155 3.7327 5.5817
Pocillopora_meandrina_HIv1___xfSc0000527 44235 270300 6.1105 8.5079
Pocillopora_meandrina_HIv1___xfSc0000540 43935 310767 7.0733 9.3035
Pocillopora_meandrina_HIv1___xfSc0000555 43535 266887 6.1304 11.7407
Pocillopora_meandrina_HIv1___xfSc0000565 43357 269053 6.2055 6.6503
Pocillopora_meandrina_HIv1___xfSc0000566 43316 189675 4.3789 6.6349
Pocillopora_meandrina_HIv1___xfSc0000567 43305 176973 4.0867 7.6511
Pocillopora_meandrina_HIv1___xfSc0000570 43295 89767 2.0734 5.573
Pocillopora_meandrina_HIv1___xfSc0000579 43029 97844 2.2739 4.8431
Pocillopora_meandrina_HIv1___xfSc0000583 42958 345672 8.0467 9.1328
Pocillopora_meandrina_HIv1___xfSc0000596 42675 205122 4.8066 8.8306
Pocillopora_meandrina_HIv1___xfSc0000612 42423 103068 2.4295 3.8968
Pocillopora_meandrina_HIv1___xfSc0000616 42355 5529806 130.5585 437.4906
Pocillopora_meandrina_HIv1___xfSc0000621 42164 217703 5.1632 6.4236
Pocillopora_meandrina_HIv1___xfSc0000642 41754 160343 3.8402 6.9183
Pocillopora_meandrina_HIv1___xfSc0000655 41446 157346 3.7964 6.6498
Pocillopora_meandrina_HIv1___xfSc0000692 40426 52044 1.2874 4.1408
Pocillopora_meandrina_HIv1___xfSc0000699 40296 74307 1.844 3.8898
Pocillopora_meandrina_HIv1___xfSc0000704 40233 448636 11.1509 15.915
Pocillopora_meandrina_HIv1___xfSc0000705 40197 92606 2.3038 4.3755
Pocillopora_meandrina_HIv1___xfSc0000716 39998 391343 9.7841 9.9697
Pocillopora_meandrina_HIv1___xfSc0000725 39827 102900 2.5837 8.6038
Pocillopora_meandrina_HIv1___xfSc0000729 39775 18980 0.4772 3.4272
Pocillopora_meandrina_HIv1___xfSc0000760 39228 17810 0.454 2.0626
Pocillopora_meandrina_HIv1___xfSc0000763 39151 240178 6.1347 6.6655
Pocillopora_meandrina_HIv1___xfSc0000765 39117 106392 2.7198 7.6032
Pocillopora_meandrina_HIv1___xfSc0000788 38513 421325 10.9398 14.1485
Pocillopora_meandrina_HIv1___xfSc0000811 37888 182548 4.8181 5.5701
Pocillopora_meandrina_HIv1___xfSc0000812 37881 16443 0.4341 0.9451
Pocillopora_meandrina_HIv1___xfSc0000817 37779 631026 16.7031 11.6203
Pocillopora_meandrina_HIv1___xfSc0000824 37656 147568 3.9188 5.8735
Pocillopora_meandrina_HIv1___xfSc0000835 37434 228533 6.105 7.6679
Pocillopora_meandrina_HIv1___xfSc0000836 37372 194293 5.1989 8.1758
Pocillopora_meandrina_HIv1___xfSc0000837 37368 231199 6.1871 10.8651
Pocillopora_meandrina_HIv1___xfSc0000840 37283 295420 7.9237 12.288
Pocillopora_meandrina_HIv1___xfSc0000857 37006 217286 5.8716 9.4564
Pocillopora_meandrina_HIv1___xfSc0000859 36995 60024 1.6225 2.8598
Pocillopora_meandrina_HIv1___xfSc0000866 36925 57926 1.5687 3.7007
Pocillopora_meandrina_HIv1___xfSc0000868 36831 143712 3.9019 8.2589
Pocillopora_meandrina_HIv1___xfSc0000875 36611 33595 0.9176 2.5162
Pocillopora_meandrina_HIv1___xfSc0000885 36416 286175 7.8585 10.8239
Pocillopora_meandrina_HIv1___xfSc0000886 36355 164878 4.5352 7.3487
Pocillopora_meandrina_HIv1___xfSc0000890 36339 218059 6.0007 8.618
Pocillopora_meandrina_HIv1___xfSc0000892 36267 198257 5.4666 27.0746
Pocillopora_meandrina_HIv1___xfSc0000943 35168 13566 0.3857 1.7917
Pocillopora_meandrina_HIv1___xfSc0000948 35100 240746 6.8589 10.3356
Pocillopora_meandrina_HIv1___xfSc0000952 34934 317129 9.0779 7.2347
Pocillopora_meandrina_HIv1___xfSc0000953 34905 199688 5.7209 7.2349
Pocillopora_meandrina_HIv1___xfSc0000957 34773 187399 5.3892 10.4226
Pocillopora_meandrina_HIv1___xfSc0000968 34345 11978 0.3488 1.647
Pocillopora_meandrina_HIv1___xfSc0000974 34140 244359 7.1576 7.4071
Pocillopora_meandrina_HIv1___xfSc0000975 33988 345043 10.1519 9.7388
Pocillopora_meandrina_HIv1___xfSc0000995 33324 123670 3.7111 8.5444
Pocillopora_meandrina_HIv1___xfSc0001011 32918 74440 2.2614 4.4948
Pocillopora_meandrina_HIv1___xfSc0001122 29140 322248 11.0586 12.5318
Pocillopora_meandrina_HIv1___xfSc0001170 27381 17672 0.6454 1.7697
Pocillopora_meandrina_HIv1___xfSc0001179 27200 94219 3.4639 5.7582
Pocillopora_meandrina_HIv1___xfSc0001231 22938 20633 0.8995 1.4121
Pocillopora_meandrina_HIv1___xfSc0001237 22715 54948 2.419 6.4478
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1859449 4.5545 8.4112
Pocillopora_meandrina_HIv1___xpSc0001275 48561 215285 4.4333 8.8561
Pocillopora_meandrina_HIv1___xpSc0001276 38618 82654 2.1403 5.1777
Pocillopora_meandrina_HIv1___xpSc0001280 35955 215924 6.0054 9.5542
Pocillopora_meandrina_HIv1___xpSc0001281 34238 277107 8.0936 14.7872
Pocillopora_meandrina_HIv1___xpSc0001290 28931 826796 28.5782 25.7119
Pocillopora_meandrina_HIv1___xpSc0001321 15304 53713 3.5097 7.4225
Pocillopora_meandrina_HIv1___xpSc0001331 8958 159853 17.8447 11.4796
Pocillopora_meandrina_HIv1___xpSc0001337 6786 81337 11.986 5.9459
Pocillopora_meandrina_HIv1___xpSc0001344 5647 44954 7.9607 11.9696
Pocillopora_meandrina_HIv1___xpSc0001355 3576 31864 8.9105 7.0032

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 21:12:03
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