Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-219-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-219-TP4_R1_001.fastp-trim.fq.gz -2 POC-219-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-219-TP4 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 01:05:57 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-219-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 53,730,996
Mapped reads 53,730,996 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 53,730,996 / 100%
Mapped reads, first in pair 26,865,498 / 50%
Mapped reads, second in pair 26,865,498 / 50%
Mapped reads, both in pair 53,730,996 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 129.77
Overlapping read pairs 19,798,546 / 73.7%
Duplicated reads (estimated) 7,573,941 / 14.1%
Duplication rate 13.48%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,780,680,890 / 40.05%
Number/percentage of C's 696,011,715 / 10.03%
Number/percentage of T's 2,784,261,308 / 40.1%
Number/percentage of G's 681,195,907 / 9.81%
Number/percentage of N's 598,603 / 0.01%
GC Percentage 19.84%

Coverage

Mean 18.4932
Standard Deviation 20.4336
Mean (paired-end reads overlap ignored) 14.59

Mapping Quality

Mean Mapping Quality 22.69

Insert size

Mean 220.73
Standard Deviation 82.12
P25/Median/P75 152 / 211 / 272

Mismatches and indels

General error rate 21.34%
Mismatches 1,456,420,444
Insertions 9,957,991
Mapped reads with at least one insertion 13.95%
Deletions 7,932,358
Mapped reads with at least one deletion 12.42%
Homopolymer indels 51.85%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 435150386 20.0983 15.5651
Pocillopora_meandrina_HIv1___Sc0000001 21507942 455112073 21.1602 15.0438
Pocillopora_meandrina_HIv1___Sc0000002 19741974 403947115 20.4613 14.2741
Pocillopora_meandrina_HIv1___Sc0000003 19417450 353148393 18.1872 16.6116
Pocillopora_meandrina_HIv1___Sc0000004 14584444 263691743 18.0803 33.6557
Pocillopora_meandrina_HIv1___Sc0000005 14098929 282507451 20.0375 13.7754
Pocillopora_meandrina_HIv1___Sc0000006 14068054 283338899 20.1406 16.7354
Pocillopora_meandrina_HIv1___Sc0000007 13590779 267019815 19.6471 15.5438
Pocillopora_meandrina_HIv1___Sc0000008 12446599 257854874 20.7169 14.6904
Pocillopora_meandrina_HIv1___Sc0000009 11983232 141010740 11.7673 28.0095
Pocillopora_meandrina_HIv1___Sc0000010 11763137 215648523 18.3326 17.567
Pocillopora_meandrina_HIv1___Sc0000011 10501528 241504341 22.9971 13.0027
Pocillopora_meandrina_HIv1___Sc0000012 10024633 196156110 19.5674 23.3554
Pocillopora_meandrina_HIv1___Sc0000013 9946974 139538194 14.0282 14.7687
Pocillopora_meandrina_HIv1___Sc0000014 9536826 203491818 21.3375 14.1159
Pocillopora_meandrina_HIv1___Sc0000015 9393205 182343003 19.4122 14.52
Pocillopora_meandrina_HIv1___Sc0000016 9288165 168170356 18.1059 14.6466
Pocillopora_meandrina_HIv1___Sc0000017 9274345 173667362 18.7256 13.8684
Pocillopora_meandrina_HIv1___Sc0000018 8584156 173335848 20.1925 13.904
Pocillopora_meandrina_HIv1___Sc0000019 7112774 135996655 19.1201 16.1367
Pocillopora_meandrina_HIv1___Sc0000020 6748058 137603565 20.3916 18.501
Pocillopora_meandrina_HIv1___Sc0000021 6546105 138968186 21.2291 15.5464
Pocillopora_meandrina_HIv1___Sc0000022 6319256 111658989 17.6696 20.6547
Pocillopora_meandrina_HIv1___Sc0000023 5767069 82865487 14.3687 13.8802
Pocillopora_meandrina_HIv1___Sc0000024 5762297 66588135 11.5558 14.3568
Pocillopora_meandrina_HIv1___Sc0000025 5759531 96359001 16.7304 17.1906
Pocillopora_meandrina_HIv1___Sc0000026 5647578 129298007 22.8944 13.5617
Pocillopora_meandrina_HIv1___Sc0000027 5550630 93302457 16.8093 18.1425
Pocillopora_meandrina_HIv1___Sc0000028 5130920 108169953 21.082 15.6439
Pocillopora_meandrina_HIv1___Sc0000029 4860867 77564708 15.957 14.3707
Pocillopora_meandrina_HIv1___Sc0000030 4843735 99663079 20.5757 13.4759
Pocillopora_meandrina_HIv1___Sc0000031 4691590 91505745 19.5042 13.7179
Pocillopora_meandrina_HIv1___Sc0000032 3615800 75804818 20.9649 14.6984
Pocillopora_meandrina_HIv1___Sc0000033 3306609 48102401 14.5474 14.2307
Pocillopora_meandrina_HIv1___Sc0000034 3122802 63245145 20.2527 15.0719
Pocillopora_meandrina_HIv1___Sc0000035 3015365 41910324 13.8989 14.7697
Pocillopora_meandrina_HIv1___Sc0000036 3007169 71270686 23.7003 14.4631
Pocillopora_meandrina_HIv1___Sc0000037 2860435 55357297 19.3528 16.1266
Pocillopora_meandrina_HIv1___Sc0000038 2701138 46190723 17.1005 15.487
Pocillopora_meandrina_HIv1___Sc0000039 2599273 39131758 15.0549 15.6788
Pocillopora_meandrina_HIv1___Sc0000040 2445666 45660147 18.6698 17.9426
Pocillopora_meandrina_HIv1___Sc0000041 2159376 45805100 21.2122 13.9047
Pocillopora_meandrina_HIv1___Sc0000042 1957488 32786668 16.7494 14.6109
Pocillopora_meandrina_HIv1___Sc0000043 1845599 33180005 17.9779 14.6401
Pocillopora_meandrina_HIv1___Sc0000044 1724711 35319090 20.4783 15.2609
Pocillopora_meandrina_HIv1___Sc0000045 1153740 18224934 15.7964 13.7129
Pocillopora_meandrina_HIv1___Sc0000046 755410 10666674 14.1204 27.1073
Pocillopora_meandrina_HIv1___Sc0000047 239089 185126 0.7743 2.3173
Pocillopora_meandrina_HIv1___Sc0000048 214660 49640 0.2312 1.5825
Pocillopora_meandrina_HIv1___Sc0000049 179266 169920 0.9479 3.3134
Pocillopora_meandrina_HIv1___Sc0000050 177168 329605 1.8604 6.9194
Pocillopora_meandrina_HIv1___Sc0000051 165057 1569582 9.5093 15.41
Pocillopora_meandrina_HIv1___Sc0000052 155210 104900 0.6759 8.218
Pocillopora_meandrina_HIv1___Sc0000053 123249 345716 2.805 8.5285
Pocillopora_meandrina_HIv1___Sc0000054 122643 1836490 14.9743 16.3196
Pocillopora_meandrina_HIv1___Sc0000055 121609 738457 6.0724 11.9441
Pocillopora_meandrina_HIv1___Sc0000056 112816 98890 0.8766 9.5981
Pocillopora_meandrina_HIv1___Sc0000057 107171 353033 3.2941 7.578
Pocillopora_meandrina_HIv1___Sc0000058 98341 72030 0.7325 7.853
Pocillopora_meandrina_HIv1___Sc0000059 83292 2885 0.0346 0.2319
Pocillopora_meandrina_HIv1___Sc0000060 79483 681 0.0086 0.1224
Pocillopora_meandrina_HIv1___Sc0000061 75390 463402 6.1467 14.6846
Pocillopora_meandrina_HIv1___Sc0000062 74194 28920 0.3898 1.6426
Pocillopora_meandrina_HIv1___Sc0000063 73457 150193 2.0446 20.9562
Pocillopora_meandrina_HIv1___Sc0000064 72700 14322 0.197 1.0752
Pocillopora_meandrina_HIv1___Sc0000065 67986 7806 0.1148 1.4492
Pocillopora_meandrina_HIv1___Sc0000066 66659 520821 7.8132 8.6864
Pocillopora_meandrina_HIv1___Sc0000067 64947 214063 3.296 7.1896
Pocillopora_meandrina_HIv1___Sc0000068 64340 10739 0.1669 1.2215
Pocillopora_meandrina_HIv1___Sc0000069 62616 218135 3.4837 9.2085
Pocillopora_meandrina_HIv1___Sc0000070 60121 137660 2.2897 11.1402
Pocillopora_meandrina_HIv1___Sc0000071 57157 57556 1.007 2.7786
Pocillopora_meandrina_HIv1___Sc0000072 56626 23681 0.4182 5.1746
Pocillopora_meandrina_HIv1___Sc0000073 56082 15826 0.2822 1.3257
Pocillopora_meandrina_HIv1___Sc0000074 55210 797 0.0144 0.1928
Pocillopora_meandrina_HIv1___Sc0000075 54685 1212 0.0222 0.2222
Pocillopora_meandrina_HIv1___Sc0000076 54587 260999 4.7813 24.4125
Pocillopora_meandrina_HIv1___Sc0000077 53379 26707 0.5003 1.203
Pocillopora_meandrina_HIv1___Sc0000078 51564 562 0.0109 0.1172
Pocillopora_meandrina_HIv1___Sc0000079 49664 2693 0.0542 0.3175
Pocillopora_meandrina_HIv1___Sc0000080 47218 129983 2.7528 8.5529
Pocillopora_meandrina_HIv1___Sc0000081 42490 12097 0.2847 1.0469
Pocillopora_meandrina_HIv1___Sc0000082 32657 811810 24.8587 54.5541
Pocillopora_meandrina_HIv1___Sc0000083 27992 4489 0.1604 0.7732
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 21176481 13.222 20.764
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 2411034 2.013 5.2198
Pocillopora_meandrina_HIv1___xfSc0000002 779520 8449286 10.8391 14.0202
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1234615 2.6703 5.2197
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1438843 4.2979 7.679
Pocillopora_meandrina_HIv1___xfSc0000006 290100 543272 1.8727 4.809
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1360053 5.3915 8.2524
Pocillopora_meandrina_HIv1___xfSc0000012 148278 614550 4.1446 8.6372
Pocillopora_meandrina_HIv1___xfSc0000014 118081 25182 0.2133 1.0113
Pocillopora_meandrina_HIv1___xfSc0000017 98555 1155715 11.7266 190.3244
Pocillopora_meandrina_HIv1___xfSc0000021 95778 537845 5.6155 12.5379
Pocillopora_meandrina_HIv1___xfSc0000024 90744 990916 10.9199 19.3622
Pocillopora_meandrina_HIv1___xfSc0000029 85532 351796 4.113 10.0236
Pocillopora_meandrina_HIv1___xfSc0000038 77395 26317 0.34 2.4067
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1444616 20.7208 22.9319
Pocillopora_meandrina_HIv1___xfSc0000059 69426 925492 13.3306 10.5842
Pocillopora_meandrina_HIv1___xfSc0000074 66573 232699 3.4954 7.6672
Pocillopora_meandrina_HIv1___xfSc0000081 65415 442232 6.7604 7.8337
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1160647 17.7694 15.4782
Pocillopora_meandrina_HIv1___xfSc0000092 63607 864006 13.5835 11.9272
Pocillopora_meandrina_HIv1___xfSc0000094 62842 133577 2.1256 4.9391
Pocillopora_meandrina_HIv1___xfSc0000113 60556 845237 13.9579 14.1478
Pocillopora_meandrina_HIv1___xfSc0000132 59032 89148 1.5102 4.0578
Pocillopora_meandrina_HIv1___xfSc0000145 58221 195732 3.3619 6.5591
Pocillopora_meandrina_HIv1___xfSc0000146 58151 110835 1.906 5.1377
Pocillopora_meandrina_HIv1___xfSc0000168 56681 391879 6.9138 10.841
Pocillopora_meandrina_HIv1___xfSc0000175 56271 273108 4.8534 12.8982
Pocillopora_meandrina_HIv1___xfSc0000195 55223 7140 0.1293 1.1076
Pocillopora_meandrina_HIv1___xfSc0000199 55095 474409 8.6107 15.0927
Pocillopora_meandrina_HIv1___xfSc0000205 54658 165842 3.0342 5.0943
Pocillopora_meandrina_HIv1___xfSc0000206 54623 253462 4.6402 7.2529
Pocillopora_meandrina_HIv1___xfSc0000212 54299 404423 7.4481 12.5081
Pocillopora_meandrina_HIv1___xfSc0000217 54168 473591 8.743 20.558
Pocillopora_meandrina_HIv1___xfSc0000223 53823 443156 8.2336 9.4299
Pocillopora_meandrina_HIv1___xfSc0000228 53382 492640 9.2286 32.1899
Pocillopora_meandrina_HIv1___xfSc0000237 53049 338731 6.3852 9.3565
Pocillopora_meandrina_HIv1___xfSc0000262 52308 507898 9.7098 10.53
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1980981 37.9034 33.1362
Pocillopora_meandrina_HIv1___xfSc0000272 52107 546764 10.4931 14.4004
Pocillopora_meandrina_HIv1___xfSc0000275 51938 557364 10.7313 13.2094
Pocillopora_meandrina_HIv1___xfSc0000284 51483 384376 7.4661 11.2464
Pocillopora_meandrina_HIv1___xfSc0000288 51367 750411 14.6088 15.142
Pocillopora_meandrina_HIv1___xfSc0000300 50845 11001 0.2164 0.7459
Pocillopora_meandrina_HIv1___xfSc0000301 50809 605746 11.922 13.9683
Pocillopora_meandrina_HIv1___xfSc0000343 49544 209944 4.2375 7.4589
Pocillopora_meandrina_HIv1___xfSc0000376 48519 526250 10.8463 32.3674
Pocillopora_meandrina_HIv1___xfSc0000415 47398 229695 4.8461 6.4845
Pocillopora_meandrina_HIv1___xfSc0000423 47202 58981 1.2495 3.5506
Pocillopora_meandrina_HIv1___xfSc0000426 47096 960355 20.3914 24.5722
Pocillopora_meandrina_HIv1___xfSc0000428 47057 301111 6.3989 12.8644
Pocillopora_meandrina_HIv1___xfSc0000436 46816 309346 6.6077 11.3671
Pocillopora_meandrina_HIv1___xfSc0000445 46561 119278 2.5618 5.3767
Pocillopora_meandrina_HIv1___xfSc0000447 46542 552426 11.8694 14.13
Pocillopora_meandrina_HIv1___xfSc0000469 45938 458569 9.9823 10.0042
Pocillopora_meandrina_HIv1___xfSc0000477 45781 203216 4.4389 7.8057
Pocillopora_meandrina_HIv1___xfSc0000479 45736 176260 3.8539 6.2257
Pocillopora_meandrina_HIv1___xfSc0000482 45585 492470 10.8033 16.6186
Pocillopora_meandrina_HIv1___xfSc0000488 45379 121869 2.6856 5.1576
Pocillopora_meandrina_HIv1___xfSc0000506 44781 181245 4.0474 6.3999
Pocillopora_meandrina_HIv1___xfSc0000527 44235 272535 6.1611 8.4092
Pocillopora_meandrina_HIv1___xfSc0000540 43935 403350 9.1806 11.9504
Pocillopora_meandrina_HIv1___xfSc0000555 43535 291635 6.6989 13.5331
Pocillopora_meandrina_HIv1___xfSc0000565 43357 373825 8.622 8.4246
Pocillopora_meandrina_HIv1___xfSc0000566 43316 293395 6.7734 11.727
Pocillopora_meandrina_HIv1___xfSc0000567 43305 237167 5.4767 10.0734
Pocillopora_meandrina_HIv1___xfSc0000570 43295 76894 1.776 4.7325
Pocillopora_meandrina_HIv1___xfSc0000579 43029 85250 1.9812 4.9815
Pocillopora_meandrina_HIv1___xfSc0000583 42958 376400 8.762 9.5797
Pocillopora_meandrina_HIv1___xfSc0000596 42675 212305 4.9749 8.6828
Pocillopora_meandrina_HIv1___xfSc0000612 42423 126221 2.9753 4.855
Pocillopora_meandrina_HIv1___xfSc0000616 42355 10848126 256.1239 917.8965
Pocillopora_meandrina_HIv1___xfSc0000621 42164 517189 12.2661 12.8243
Pocillopora_meandrina_HIv1___xfSc0000642 41754 466156 11.1643 15.7131
Pocillopora_meandrina_HIv1___xfSc0000655 41446 752278 18.1508 38.7159
Pocillopora_meandrina_HIv1___xfSc0000692 40426 57318 1.4178 5.3568
Pocillopora_meandrina_HIv1___xfSc0000699 40296 25934 0.6436 1.8022
Pocillopora_meandrina_HIv1___xfSc0000704 40233 224147 5.5712 10.707
Pocillopora_meandrina_HIv1___xfSc0000705 40197 142406 3.5427 6.7225
Pocillopora_meandrina_HIv1___xfSc0000716 39998 483592 12.0904 12.9598
Pocillopora_meandrina_HIv1___xfSc0000725 39827 94547 2.3739 7.0756
Pocillopora_meandrina_HIv1___xfSc0000729 39775 28418 0.7145 4.6483
Pocillopora_meandrina_HIv1___xfSc0000760 39228 9933 0.2532 1.2034
Pocillopora_meandrina_HIv1___xfSc0000763 39151 293195 7.4888 8.523
Pocillopora_meandrina_HIv1___xfSc0000765 39117 77280 1.9756 6.5377
Pocillopora_meandrina_HIv1___xfSc0000788 38513 372940 9.6835 10.835
Pocillopora_meandrina_HIv1___xfSc0000811 37888 602514 15.9025 15.442
Pocillopora_meandrina_HIv1___xfSc0000812 37881 29190 0.7706 2.2615
Pocillopora_meandrina_HIv1___xfSc0000817 37779 492034 13.024 11.4429
Pocillopora_meandrina_HIv1___xfSc0000824 37656 128826 3.4211 5.7726
Pocillopora_meandrina_HIv1___xfSc0000835 37434 137647 3.6771 6.7838
Pocillopora_meandrina_HIv1___xfSc0000836 37372 317653 8.4998 13.1803
Pocillopora_meandrina_HIv1___xfSc0000837 37368 405239 10.8445 13.8321
Pocillopora_meandrina_HIv1___xfSc0000840 37283 340843 9.142 15.7612
Pocillopora_meandrina_HIv1___xfSc0000857 37006 181740 4.9111 6.8343
Pocillopora_meandrina_HIv1___xfSc0000859 36995 93566 2.5292 5.5708
Pocillopora_meandrina_HIv1___xfSc0000866 36925 73391 1.9876 3.7686
Pocillopora_meandrina_HIv1___xfSc0000868 36831 106487 2.8912 7.0815
Pocillopora_meandrina_HIv1___xfSc0000875 36611 25766 0.7038 2.227
Pocillopora_meandrina_HIv1___xfSc0000885 36416 228164 6.2655 9.3843
Pocillopora_meandrina_HIv1___xfSc0000886 36355 65961 1.8144 5.4849
Pocillopora_meandrina_HIv1___xfSc0000890 36339 266745 7.3405 12.14
Pocillopora_meandrina_HIv1___xfSc0000892 36267 79813 2.2007 10.6737
Pocillopora_meandrina_HIv1___xfSc0000943 35168 7773 0.221 1.2421
Pocillopora_meandrina_HIv1___xfSc0000948 35100 281534 8.0209 11.422
Pocillopora_meandrina_HIv1___xfSc0000952 34934 222023 6.3555 8.1733
Pocillopora_meandrina_HIv1___xfSc0000953 34905 197148 5.6481 8.0035
Pocillopora_meandrina_HIv1___xfSc0000957 34773 144925 4.1677 7.799
Pocillopora_meandrina_HIv1___xfSc0000968 34345 27211 0.7923 3.5476
Pocillopora_meandrina_HIv1___xfSc0000974 34140 304455 8.9178 9.8557
Pocillopora_meandrina_HIv1___xfSc0000975 33988 596774 17.5584 20.7579
Pocillopora_meandrina_HIv1___xfSc0000995 33324 171942 5.1597 10.9257
Pocillopora_meandrina_HIv1___xfSc0001011 32918 250395 7.6066 14.2639
Pocillopora_meandrina_HIv1___xfSc0001122 29140 336955 11.5633 11.1111
Pocillopora_meandrina_HIv1___xfSc0001170 27381 32573 1.1896 3.7564
Pocillopora_meandrina_HIv1___xfSc0001179 27200 110996 4.0807 6.9353
Pocillopora_meandrina_HIv1___xfSc0001231 22938 17679 0.7707 1.6031
Pocillopora_meandrina_HIv1___xfSc0001237 22715 44742 1.9697 6.4095
Pocillopora_meandrina_HIv1___xpSc0001273 408270 906091 2.2193 6.1997
Pocillopora_meandrina_HIv1___xpSc0001275 48561 233302 4.8043 9.4417
Pocillopora_meandrina_HIv1___xpSc0001276 38618 41509 1.0749 3.4036
Pocillopora_meandrina_HIv1___xpSc0001280 35955 99322 2.7624 4.362
Pocillopora_meandrina_HIv1___xpSc0001281 34238 206024 6.0174 8.736
Pocillopora_meandrina_HIv1___xpSc0001290 28931 206173 7.1264 8.5945
Pocillopora_meandrina_HIv1___xpSc0001321 15304 116417 7.607 13.1854
Pocillopora_meandrina_HIv1___xpSc0001331 8958 219742 24.5303 13.1986
Pocillopora_meandrina_HIv1___xpSc0001337 6786 25623 3.7759 8.3676
Pocillopora_meandrina_HIv1___xpSc0001344 5647 56913 10.0784 15.5355
Pocillopora_meandrina_HIv1___xpSc0001355 3576 74716 20.8937 10.573

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 01:05:58
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