Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-222-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-222-TP3_R1_001.fastp-trim.fq.gz -2 POC-222-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-222-TP3 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:20:54 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-222-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 63,278,974
Mapped reads 63,278,974 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 63,278,974 / 100%
Mapped reads, first in pair 31,639,487 / 50%
Mapped reads, second in pair 31,639,487 / 50%
Mapped reads, both in pair 63,278,974 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.29
Overlapping read pairs 19,437,841 / 61.44%
Duplicated reads (estimated) 9,632,346 / 15.22%
Duplication rate 14.69%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 3,328,902,163 / 40.24%
Number/percentage of C's 814,597,316 / 9.85%
Number/percentage of T's 3,329,160,669 / 40.25%
Number/percentage of G's 798,301,701 / 9.65%
Number/percentage of N's 687,268 / 0.01%
GC Percentage 19.5%

Coverage

Mean 22.0346
Standard Deviation 22.75
Mean (paired-end reads overlap ignored) 18.53

Mapping Quality

Mean Mapping Quality 22.76

Insert size

Mean 247.25
Standard Deviation 88.2
P25/Median/P75 179 / 242 / 305

Mismatches and indels

General error rate 21.23%
Mismatches 1,725,655,486
Insertions 12,079,213
Mapped reads with at least one insertion 14.43%
Deletions 9,701,551
Mapped reads with at least one deletion 12.88%
Homopolymer indels 52.25%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 510261304 23.5674 16.7331
Pocillopora_meandrina_HIv1___Sc0000001 21507942 532143397 24.7417 15.9134
Pocillopora_meandrina_HIv1___Sc0000002 19741974 480337957 24.3308 16.3468
Pocillopora_meandrina_HIv1___Sc0000003 19417450 402232177 20.715 17.7005
Pocillopora_meandrina_HIv1___Sc0000004 14584444 317858700 21.7944 30.3621
Pocillopora_meandrina_HIv1___Sc0000005 14098929 335336089 23.7845 15.6781
Pocillopora_meandrina_HIv1___Sc0000006 14068054 333481340 23.7049 18.739
Pocillopora_meandrina_HIv1___Sc0000007 13590779 322828196 23.7535 18.561
Pocillopora_meandrina_HIv1___Sc0000008 12446599 309799031 24.8903 17.2573
Pocillopora_meandrina_HIv1___Sc0000009 11983232 148775409 12.4153 20.9228
Pocillopora_meandrina_HIv1___Sc0000010 11763137 254121884 21.6032 20.6141
Pocillopora_meandrina_HIv1___Sc0000011 10501528 287761752 27.4019 15.7463
Pocillopora_meandrina_HIv1___Sc0000012 10024633 234616452 23.404 37.3078
Pocillopora_meandrina_HIv1___Sc0000013 9946974 176392669 17.7333 17.2024
Pocillopora_meandrina_HIv1___Sc0000014 9536826 237982776 24.9541 16.1088
Pocillopora_meandrina_HIv1___Sc0000015 9393205 211648558 22.5321 16.2927
Pocillopora_meandrina_HIv1___Sc0000016 9288165 209370768 22.5417 17.2703
Pocillopora_meandrina_HIv1___Sc0000017 9274345 209953381 22.6381 16.3385
Pocillopora_meandrina_HIv1___Sc0000018 8584156 205476830 23.9368 16.0503
Pocillopora_meandrina_HIv1___Sc0000019 7112774 160400822 22.5511 17.9824
Pocillopora_meandrina_HIv1___Sc0000020 6748058 150049953 22.236 16.4123
Pocillopora_meandrina_HIv1___Sc0000021 6546105 159749429 24.4037 16.8931
Pocillopora_meandrina_HIv1___Sc0000022 6319256 133260008 21.0879 21.0614
Pocillopora_meandrina_HIv1___Sc0000023 5767069 111744883 19.3764 17.5013
Pocillopora_meandrina_HIv1___Sc0000024 5762297 85309623 14.8048 21.4443
Pocillopora_meandrina_HIv1___Sc0000025 5759531 118351273 20.5488 21.6794
Pocillopora_meandrina_HIv1___Sc0000026 5647578 152696696 27.0376 15.5568
Pocillopora_meandrina_HIv1___Sc0000027 5550630 126379548 22.7685 27.1015
Pocillopora_meandrina_HIv1___Sc0000028 5130920 134214417 26.158 22.557
Pocillopora_meandrina_HIv1___Sc0000029 4860867 91675237 18.8599 16.4311
Pocillopora_meandrina_HIv1___Sc0000030 4843735 120800734 24.9396 15.2496
Pocillopora_meandrina_HIv1___Sc0000031 4691590 114003438 24.2995 16.6089
Pocillopora_meandrina_HIv1___Sc0000032 3615800 94874732 26.2389 17.9421
Pocillopora_meandrina_HIv1___Sc0000033 3306609 58372620 17.6533 16.5955
Pocillopora_meandrina_HIv1___Sc0000034 3122802 76875283 24.6174 17.5775
Pocillopora_meandrina_HIv1___Sc0000035 3015365 56623453 18.7783 18.9645
Pocillopora_meandrina_HIv1___Sc0000036 3007169 84280733 28.0266 15.7961
Pocillopora_meandrina_HIv1___Sc0000037 2860435 67708943 23.6709 32.3952
Pocillopora_meandrina_HIv1___Sc0000038 2701138 58454456 21.6407 17.1606
Pocillopora_meandrina_HIv1___Sc0000039 2599273 45348747 17.4467 17.6337
Pocillopora_meandrina_HIv1___Sc0000040 2445666 56955626 23.2884 21.427
Pocillopora_meandrina_HIv1___Sc0000041 2159376 54991885 25.4666 15.3345
Pocillopora_meandrina_HIv1___Sc0000042 1957488 39082349 19.9656 16.7269
Pocillopora_meandrina_HIv1___Sc0000043 1845599 34738007 18.8221 15.9036
Pocillopora_meandrina_HIv1___Sc0000044 1724711 42765773 24.7959 18.7155
Pocillopora_meandrina_HIv1___Sc0000045 1153740 23908187 20.7223 18.6035
Pocillopora_meandrina_HIv1___Sc0000046 755410 12112605 16.0345 23.614
Pocillopora_meandrina_HIv1___Sc0000047 239089 166018 0.6944 2.5114
Pocillopora_meandrina_HIv1___Sc0000048 214660 62054 0.2891 1.7508
Pocillopora_meandrina_HIv1___Sc0000049 179266 1157574 6.4573 14.028
Pocillopora_meandrina_HIv1___Sc0000050 177168 313051 1.767 4.1256
Pocillopora_meandrina_HIv1___Sc0000051 165057 1013538 6.1405 11.1225
Pocillopora_meandrina_HIv1___Sc0000052 155210 162456 1.0467 11.1505
Pocillopora_meandrina_HIv1___Sc0000053 123249 400819 3.2521 7.6678
Pocillopora_meandrina_HIv1___Sc0000054 122643 2196950 17.9134 19.511
Pocillopora_meandrina_HIv1___Sc0000055 121609 821871 6.7583 14.5568
Pocillopora_meandrina_HIv1___Sc0000056 112816 105108 0.9317 9.7057
Pocillopora_meandrina_HIv1___Sc0000057 107171 393974 3.6761 9.0058
Pocillopora_meandrina_HIv1___Sc0000058 98341 125586 1.277 12.6756
Pocillopora_meandrina_HIv1___Sc0000059 83292 11960 0.1436 0.6829
Pocillopora_meandrina_HIv1___Sc0000060 79483 514 0.0065 0.1054
Pocillopora_meandrina_HIv1___Sc0000061 75390 387209 5.1361 10.7745
Pocillopora_meandrina_HIv1___Sc0000062 74194 26191 0.353 1.3957
Pocillopora_meandrina_HIv1___Sc0000063 73457 118843 1.6179 16.2748
Pocillopora_meandrina_HIv1___Sc0000064 72700 16189 0.2227 1.102
Pocillopora_meandrina_HIv1___Sc0000065 67986 3173 0.0467 0.3074
Pocillopora_meandrina_HIv1___Sc0000066 66659 670374 10.0568 10.3776
Pocillopora_meandrina_HIv1___Sc0000067 64947 175910 2.7085 5.911
Pocillopora_meandrina_HIv1___Sc0000068 64340 10364 0.1611 1.0758
Pocillopora_meandrina_HIv1___Sc0000069 62616 273800 4.3727 11.2594
Pocillopora_meandrina_HIv1___Sc0000070 60121 484896 8.0653 44.6287
Pocillopora_meandrina_HIv1___Sc0000071 57157 59423 1.0396 2.6415
Pocillopora_meandrina_HIv1___Sc0000072 56626 14777 0.261 2.8535
Pocillopora_meandrina_HIv1___Sc0000073 56082 17122 0.3053 1.0375
Pocillopora_meandrina_HIv1___Sc0000074 55210 501 0.0091 0.1032
Pocillopora_meandrina_HIv1___Sc0000075 54685 782 0.0143 0.1453
Pocillopora_meandrina_HIv1___Sc0000076 54587 280614 5.1407 26.5046
Pocillopora_meandrina_HIv1___Sc0000077 53379 38086 0.7135 1.7149
Pocillopora_meandrina_HIv1___Sc0000078 51564 258 0.005 0.0766
Pocillopora_meandrina_HIv1___Sc0000079 49664 1075 0.0216 0.1725
Pocillopora_meandrina_HIv1___Sc0000080 47218 143132 3.0313 7.441
Pocillopora_meandrina_HIv1___Sc0000081 42490 19608 0.4615 1.1636
Pocillopora_meandrina_HIv1___Sc0000082 32657 905132 27.7163 61.4102
Pocillopora_meandrina_HIv1___Sc0000083 27992 4660 0.1665 0.7213
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 10201625 6.3696 10.833
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5825492 4.8638 10.199
Pocillopora_meandrina_HIv1___xfSc0000002 779520 13732179 17.6162 23.584
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1335143 2.8878 6.204
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1966547 5.8742 9.8107
Pocillopora_meandrina_HIv1___xfSc0000006 290100 480096 1.6549 4.5409
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2328985 9.2326 12.3717
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1025855 6.9185 12.4578
Pocillopora_meandrina_HIv1___xfSc0000014 118081 26456 0.224 1.0909
Pocillopora_meandrina_HIv1___xfSc0000017 98555 754429 7.6549 114.048
Pocillopora_meandrina_HIv1___xfSc0000021 95778 748160 7.8114 13.3568
Pocillopora_meandrina_HIv1___xfSc0000024 90744 812174 8.9502 12.64
Pocillopora_meandrina_HIv1___xfSc0000029 85532 147690 1.7267 6.5909
Pocillopora_meandrina_HIv1___xfSc0000038 77395 107815 1.393 15.9824
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1371746 19.6756 21.5599
Pocillopora_meandrina_HIv1___xfSc0000059 69426 489401 7.0492 12.0862
Pocillopora_meandrina_HIv1___xfSc0000074 66573 404989 6.0834 10.3616
Pocillopora_meandrina_HIv1___xfSc0000081 65415 549521 8.4005 9.8978
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1167542 17.875 18.6536
Pocillopora_meandrina_HIv1___xfSc0000092 63607 669299 10.5224 12.0566
Pocillopora_meandrina_HIv1___xfSc0000094 62842 168115 2.6752 5.5993
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1187527 19.6104 20.9402
Pocillopora_meandrina_HIv1___xfSc0000132 59032 42931 0.7272 1.9639
Pocillopora_meandrina_HIv1___xfSc0000145 58221 789899 13.5673 12.4442
Pocillopora_meandrina_HIv1___xfSc0000146 58151 220205 3.7868 8.1974
Pocillopora_meandrina_HIv1___xfSc0000168 56681 458324 8.086 12.7308
Pocillopora_meandrina_HIv1___xfSc0000175 56271 255645 4.5431 10.4167
Pocillopora_meandrina_HIv1___xfSc0000195 55223 19913 0.3606 2.1506
Pocillopora_meandrina_HIv1___xfSc0000199 55095 346788 6.2944 10.0807
Pocillopora_meandrina_HIv1___xfSc0000205 54658 166412 3.0446 5.839
Pocillopora_meandrina_HIv1___xfSc0000206 54623 311222 5.6976 8.5601
Pocillopora_meandrina_HIv1___xfSc0000212 54299 482936 8.894 13.5235
Pocillopora_meandrina_HIv1___xfSc0000217 54168 508022 9.3786 21.1968
Pocillopora_meandrina_HIv1___xfSc0000223 53823 684526 12.7181 11.8683
Pocillopora_meandrina_HIv1___xfSc0000228 53382 385539 7.2223 36.5663
Pocillopora_meandrina_HIv1___xfSc0000237 53049 388307 7.3198 10.0261
Pocillopora_meandrina_HIv1___xfSc0000262 52308 299332 5.7225 8.0281
Pocillopora_meandrina_HIv1___xfSc0000264 52264 991099 18.9633 16.6829
Pocillopora_meandrina_HIv1___xfSc0000272 52107 610381 11.714 16.4708
Pocillopora_meandrina_HIv1___xfSc0000275 51938 713837 13.744 18.5327
Pocillopora_meandrina_HIv1___xfSc0000284 51483 708994 13.7714 16.1565
Pocillopora_meandrina_HIv1___xfSc0000288 51367 479698 9.3386 19.0112
Pocillopora_meandrina_HIv1___xfSc0000300 50845 17346 0.3412 1.1916
Pocillopora_meandrina_HIv1___xfSc0000301 50809 827375 16.284 13.1571
Pocillopora_meandrina_HIv1___xfSc0000343 49544 416057 8.3977 13.3835
Pocillopora_meandrina_HIv1___xfSc0000376 48519 671332 13.8365 43.5163
Pocillopora_meandrina_HIv1___xfSc0000415 47398 373451 7.879 11.2623
Pocillopora_meandrina_HIv1___xfSc0000423 47202 64371 1.3637 3.815
Pocillopora_meandrina_HIv1___xfSc0000426 47096 2984582 63.3723 77.0618
Pocillopora_meandrina_HIv1___xfSc0000428 47057 943927 20.0592 28.6113
Pocillopora_meandrina_HIv1___xfSc0000436 46816 402200 8.5911 13.5784
Pocillopora_meandrina_HIv1___xfSc0000445 46561 93974 2.0183 5.4486
Pocillopora_meandrina_HIv1___xfSc0000447 46542 674440 14.491 15.3497
Pocillopora_meandrina_HIv1___xfSc0000469 45938 733923 15.9764 12.9513
Pocillopora_meandrina_HIv1___xfSc0000477 45781 524902 11.4655 10.8113
Pocillopora_meandrina_HIv1___xfSc0000479 45736 215842 4.7193 8.0475
Pocillopora_meandrina_HIv1___xfSc0000482 45585 347250 7.6176 14.9759
Pocillopora_meandrina_HIv1___xfSc0000488 45379 424663 9.3581 13.0594
Pocillopora_meandrina_HIv1___xfSc0000506 44781 218111 4.8706 7.7005
Pocillopora_meandrina_HIv1___xfSc0000527 44235 328612 7.4288 10.4832
Pocillopora_meandrina_HIv1___xfSc0000540 43935 437546 9.9589 12.9804
Pocillopora_meandrina_HIv1___xfSc0000555 43535 142895 3.2823 9.0216
Pocillopora_meandrina_HIv1___xfSc0000565 43357 783473 18.0703 15.8813
Pocillopora_meandrina_HIv1___xfSc0000566 43316 446400 10.3057 20.7519
Pocillopora_meandrina_HIv1___xfSc0000567 43305 280799 6.4842 11.984
Pocillopora_meandrina_HIv1___xfSc0000570 43295 150938 3.4863 9.2808
Pocillopora_meandrina_HIv1___xfSc0000579 43029 119640 2.7805 6.3864
Pocillopora_meandrina_HIv1___xfSc0000583 42958 448621 10.4432 10.7475
Pocillopora_meandrina_HIv1___xfSc0000596 42675 1143824 26.8031 14.2065
Pocillopora_meandrina_HIv1___xfSc0000612 42423 257756 6.0759 9.9228
Pocillopora_meandrina_HIv1___xfSc0000616 42355 15850797 374.2367 992.9966
Pocillopora_meandrina_HIv1___xfSc0000621 42164 572949 13.5886 16.088
Pocillopora_meandrina_HIv1___xfSc0000642 41754 260878 6.248 8.7338
Pocillopora_meandrina_HIv1___xfSc0000655 41446 656689 15.8444 30.7768
Pocillopora_meandrina_HIv1___xfSc0000692 40426 312440 7.7287 8.8168
Pocillopora_meandrina_HIv1___xfSc0000699 40296 66187 1.6425 3.7752
Pocillopora_meandrina_HIv1___xfSc0000704 40233 928123 23.0687 30.9063
Pocillopora_meandrina_HIv1___xfSc0000705 40197 165954 4.1285 8.7245
Pocillopora_meandrina_HIv1___xfSc0000716 39998 332494 8.3128 10.3367
Pocillopora_meandrina_HIv1___xfSc0000725 39827 124816 3.134 9.9482
Pocillopora_meandrina_HIv1___xfSc0000729 39775 68248 1.7159 11.096
Pocillopora_meandrina_HIv1___xfSc0000760 39228 16395 0.4179 1.8302
Pocillopora_meandrina_HIv1___xfSc0000763 39151 327354 8.3613 8.3135
Pocillopora_meandrina_HIv1___xfSc0000765 39117 89292 2.2827 5.9792
Pocillopora_meandrina_HIv1___xfSc0000788 38513 410990 10.6715 16.4955
Pocillopora_meandrina_HIv1___xfSc0000811 37888 276672 7.3024 10.9211
Pocillopora_meandrina_HIv1___xfSc0000812 37881 34384 0.9077 1.5387
Pocillopora_meandrina_HIv1___xfSc0000817 37779 721213 19.0903 9.2235
Pocillopora_meandrina_HIv1___xfSc0000824 37656 122339 3.2489 5.5408
Pocillopora_meandrina_HIv1___xfSc0000835 37434 449567 12.0096 14.7327
Pocillopora_meandrina_HIv1___xfSc0000836 37372 328153 8.7807 15.2471
Pocillopora_meandrina_HIv1___xfSc0000837 37368 290526 7.7747 10.023
Pocillopora_meandrina_HIv1___xfSc0000840 37283 236026 6.3307 14.5564
Pocillopora_meandrina_HIv1___xfSc0000857 37006 220354 5.9545 7.0066
Pocillopora_meandrina_HIv1___xfSc0000859 36995 45631 1.2334 2.4298
Pocillopora_meandrina_HIv1___xfSc0000866 36925 85963 2.328 4.9157
Pocillopora_meandrina_HIv1___xfSc0000868 36831 138433 3.7586 8.8949
Pocillopora_meandrina_HIv1___xfSc0000875 36611 58162 1.5886 3.9596
Pocillopora_meandrina_HIv1___xfSc0000885 36416 220822 6.0639 8.1204
Pocillopora_meandrina_HIv1___xfSc0000886 36355 114834 3.1587 5.6553
Pocillopora_meandrina_HIv1___xfSc0000890 36339 276654 7.6131 10.683
Pocillopora_meandrina_HIv1___xfSc0000892 36267 338764 9.3408 46.5853
Pocillopora_meandrina_HIv1___xfSc0000943 35168 8332 0.2369 0.9567
Pocillopora_meandrina_HIv1___xfSc0000948 35100 321174 9.1503 11.7506
Pocillopora_meandrina_HIv1___xfSc0000952 34934 525982 15.0564 7.8007
Pocillopora_meandrina_HIv1___xfSc0000953 34905 287220 8.2286 11.4012
Pocillopora_meandrina_HIv1___xfSc0000957 34773 367584 10.571 18.3556
Pocillopora_meandrina_HIv1___xfSc0000968 34345 20777 0.6049 2.4824
Pocillopora_meandrina_HIv1___xfSc0000974 34140 376467 11.0272 13.6548
Pocillopora_meandrina_HIv1___xfSc0000975 33988 372494 10.9596 11.0414
Pocillopora_meandrina_HIv1___xfSc0000995 33324 117236 3.5181 9.599
Pocillopora_meandrina_HIv1___xfSc0001011 32918 218610 6.641 14.7694
Pocillopora_meandrina_HIv1___xfSc0001122 29140 524207 17.9893 16.0421
Pocillopora_meandrina_HIv1___xfSc0001170 27381 28596 1.0444 2.635
Pocillopora_meandrina_HIv1___xfSc0001179 27200 130254 4.7888 7.8932
Pocillopora_meandrina_HIv1___xfSc0001231 22938 20720 0.9033 1.6105
Pocillopora_meandrina_HIv1___xfSc0001237 22715 28959 1.2749 3.9724
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3337844 8.1756 14.0371
Pocillopora_meandrina_HIv1___xpSc0001275 48561 317878 6.546 11.4786
Pocillopora_meandrina_HIv1___xpSc0001276 38618 133441 3.4554 7.3304
Pocillopora_meandrina_HIv1___xpSc0001280 35955 98029 2.7264 4.9172
Pocillopora_meandrina_HIv1___xpSc0001281 34238 215614 6.2975 10.0312
Pocillopora_meandrina_HIv1___xpSc0001290 28931 245541 8.4871 9.5658
Pocillopora_meandrina_HIv1___xpSc0001321 15304 43498 2.8423 5.5858
Pocillopora_meandrina_HIv1___xpSc0001331 8958 206546 23.0572 12.4639
Pocillopora_meandrina_HIv1___xpSc0001337 6786 27549 4.0597 8.7587
Pocillopora_meandrina_HIv1___xpSc0001344 5647 85970 15.224 19.7021
Pocillopora_meandrina_HIv1___xpSc0001355 3576 73073 20.4343 14.3399

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 21:20:58
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