Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-57-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-57-TP2_R1_001.fastp-trim.fq.gz -2 POC-57-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-57-TP2 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 01:37:06 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-57-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 54,738,494
Mapped reads 54,738,494 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 54,738,494 / 100%
Mapped reads, first in pair 27,369,247 / 50%
Mapped reads, second in pair 27,369,247 / 50%
Mapped reads, both in pair 54,738,494 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.56
Overlapping read pairs 17,625,821 / 64.4%
Duplicated reads (estimated) 7,243,867 / 13.23%
Duplication rate 12.91%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,883,158,924 / 40.21%
Number/percentage of C's 707,580,746 / 9.87%
Number/percentage of T's 2,886,669,167 / 40.26%
Number/percentage of G's 692,175,491 / 9.65%
Number/percentage of N's 605,674 / 0.01%
GC Percentage 19.52%

Coverage

Mean 19.1003
Standard Deviation 16.2489
Mean (paired-end reads overlap ignored) 15.7

Mapping Quality

Mean Mapping Quality 22.7

Insert size

Mean 240.77
Standard Deviation 87.85
P25/Median/P75 168 / 232 / 300

Mismatches and indels

General error rate 21.18%
Mismatches 1,492,353,696
Insertions 10,346,431
Mapped reads with at least one insertion 14.3%
Deletions 8,335,108
Mapped reads with at least one deletion 12.8%
Homopolymer indels 51.94%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 443185002 20.4694 14.3617
Pocillopora_meandrina_HIv1___Sc0000001 21507942 463137438 21.5333 14.1752
Pocillopora_meandrina_HIv1___Sc0000002 19741974 418453574 21.1961 14.1381
Pocillopora_meandrina_HIv1___Sc0000003 19417450 362841520 18.6864 15.4764
Pocillopora_meandrina_HIv1___Sc0000004 14584444 273195669 18.732 23.0393
Pocillopora_meandrina_HIv1___Sc0000005 14098929 289496485 20.5332 13.6609
Pocillopora_meandrina_HIv1___Sc0000006 14068054 288931772 20.5381 15.4771
Pocillopora_meandrina_HIv1___Sc0000007 13590779 273249436 20.1055 16.1247
Pocillopora_meandrina_HIv1___Sc0000008 12446599 272865418 21.9229 15.1546
Pocillopora_meandrina_HIv1___Sc0000009 11983232 156413793 13.0527 19.1901
Pocillopora_meandrina_HIv1___Sc0000010 11763137 221851831 18.8599 16.4175
Pocillopora_meandrina_HIv1___Sc0000011 10501528 238937972 22.7527 12.2809
Pocillopora_meandrina_HIv1___Sc0000012 10024633 199331554 19.8842 16.4804
Pocillopora_meandrina_HIv1___Sc0000013 9946974 156853873 15.769 15.1666
Pocillopora_meandrina_HIv1___Sc0000014 9536826 204061771 21.3972 14.0663
Pocillopora_meandrina_HIv1___Sc0000015 9393205 181072677 19.277 13.9029
Pocillopora_meandrina_HIv1___Sc0000016 9288165 180349313 19.4171 14.8938
Pocillopora_meandrina_HIv1___Sc0000017 9274345 179487176 19.3531 14.6911
Pocillopora_meandrina_HIv1___Sc0000018 8584156 178801841 20.8293 14.0736
Pocillopora_meandrina_HIv1___Sc0000019 7112774 140879275 19.8065 15.3355
Pocillopora_meandrina_HIv1___Sc0000020 6748058 146449377 21.7024 22.3179
Pocillopora_meandrina_HIv1___Sc0000021 6546105 140630758 21.4831 14.723
Pocillopora_meandrina_HIv1___Sc0000022 6319256 117630076 18.6145 18.2181
Pocillopora_meandrina_HIv1___Sc0000023 5767069 95302901 16.5254 14.9642
Pocillopora_meandrina_HIv1___Sc0000024 5762297 75701203 13.1373 15.0724
Pocillopora_meandrina_HIv1___Sc0000025 5759531 96592089 16.7708 16.7847
Pocillopora_meandrina_HIv1___Sc0000026 5647578 132585331 23.4765 14.1556
Pocillopora_meandrina_HIv1___Sc0000027 5550630 99391322 17.9063 19.5617
Pocillopora_meandrina_HIv1___Sc0000028 5130920 117252395 22.8521 17.8606
Pocillopora_meandrina_HIv1___Sc0000029 4860867 84509170 17.3856 14.179
Pocillopora_meandrina_HIv1___Sc0000030 4843735 99963150 20.6376 13.3749
Pocillopora_meandrina_HIv1___Sc0000031 4691590 92583167 19.7339 13.5907
Pocillopora_meandrina_HIv1___Sc0000032 3615800 79904517 22.0987 15.5136
Pocillopora_meandrina_HIv1___Sc0000033 3306609 47792497 14.4536 14.5521
Pocillopora_meandrina_HIv1___Sc0000034 3122802 65427920 20.9517 14.7623
Pocillopora_meandrina_HIv1___Sc0000035 3015365 51740156 17.1588 17.1716
Pocillopora_meandrina_HIv1___Sc0000036 3007169 67788035 22.5421 12.6949
Pocillopora_meandrina_HIv1___Sc0000037 2860435 59394163 20.764 17.3545
Pocillopora_meandrina_HIv1___Sc0000038 2701138 52278905 19.3544 16.0517
Pocillopora_meandrina_HIv1___Sc0000039 2599273 40951745 15.7551 15.7591
Pocillopora_meandrina_HIv1___Sc0000040 2445666 45476956 18.5949 17.0036
Pocillopora_meandrina_HIv1___Sc0000041 2159376 45002405 20.8405 13.3765
Pocillopora_meandrina_HIv1___Sc0000042 1957488 32737262 16.7241 13.9709
Pocillopora_meandrina_HIv1___Sc0000043 1845599 29813119 16.1536 13.7913
Pocillopora_meandrina_HIv1___Sc0000044 1724711 34784417 20.1683 14.5626
Pocillopora_meandrina_HIv1___Sc0000045 1153740 19724092 17.0958 15.6054
Pocillopora_meandrina_HIv1___Sc0000046 755410 9818688 12.9978 15.9992
Pocillopora_meandrina_HIv1___Sc0000047 239089 391740 1.6385 4.9611
Pocillopora_meandrina_HIv1___Sc0000048 214660 51567 0.2402 1.362
Pocillopora_meandrina_HIv1___Sc0000049 179266 279832 1.561 6.7745
Pocillopora_meandrina_HIv1___Sc0000050 177168 218527 1.2334 3.8835
Pocillopora_meandrina_HIv1___Sc0000051 165057 859753 5.2088 8.5007
Pocillopora_meandrina_HIv1___Sc0000052 155210 93578 0.6029 7.262
Pocillopora_meandrina_HIv1___Sc0000053 123249 280655 2.2771 5.2329
Pocillopora_meandrina_HIv1___Sc0000054 122643 2003448 16.3356 17.1434
Pocillopora_meandrina_HIv1___Sc0000055 121609 515088 4.2356 9.1706
Pocillopora_meandrina_HIv1___Sc0000056 112816 65435 0.58 6.4221
Pocillopora_meandrina_HIv1___Sc0000057 107171 587910 5.4857 11.6456
Pocillopora_meandrina_HIv1___Sc0000058 98341 93603 0.9518 10.9984
Pocillopora_meandrina_HIv1___Sc0000059 83292 3131 0.0376 0.2257
Pocillopora_meandrina_HIv1___Sc0000060 79483 513 0.0065 0.1119
Pocillopora_meandrina_HIv1___Sc0000061 75390 208719 2.7685 6.1215
Pocillopora_meandrina_HIv1___Sc0000062 74194 16070 0.2166 0.9496
Pocillopora_meandrina_HIv1___Sc0000063 73457 15647 0.213 1.9986
Pocillopora_meandrina_HIv1___Sc0000064 72700 1343 0.0185 0.1501
Pocillopora_meandrina_HIv1___Sc0000065 67986 5993 0.0882 0.6582
Pocillopora_meandrina_HIv1___Sc0000066 66659 559826 8.3984 8.7224
Pocillopora_meandrina_HIv1___Sc0000067 64947 137528 2.1175 4.659
Pocillopora_meandrina_HIv1___Sc0000068 64340 10182 0.1583 1.0351
Pocillopora_meandrina_HIv1___Sc0000069 62616 212095 3.3872 8.5847
Pocillopora_meandrina_HIv1___Sc0000070 60121 290433 4.8308 27.7581
Pocillopora_meandrina_HIv1___Sc0000071 57157 68812 1.2039 2.8075
Pocillopora_meandrina_HIv1___Sc0000072 56626 13456 0.2376 2.8305
Pocillopora_meandrina_HIv1___Sc0000073 56082 9929 0.177 0.7421
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 1800 0.0329 0.2959
Pocillopora_meandrina_HIv1___Sc0000076 54587 227426 4.1663 20.5976
Pocillopora_meandrina_HIv1___Sc0000077 53379 23404 0.4384 0.9484
Pocillopora_meandrina_HIv1___Sc0000078 51564 270 0.0052 0.0722
Pocillopora_meandrina_HIv1___Sc0000079 49664 1883 0.0379 0.3394
Pocillopora_meandrina_HIv1___Sc0000080 47218 125207 2.6517 6.6703
Pocillopora_meandrina_HIv1___Sc0000081 42490 10294 0.2423 1.2725
Pocillopora_meandrina_HIv1___Sc0000082 32657 646113 19.7848 43.8968
Pocillopora_meandrina_HIv1___Sc0000083 27992 3306 0.1181 0.4808
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 9306242 5.8106 10.7613
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 7751747 6.4721 12.2364
Pocillopora_meandrina_HIv1___xfSc0000002 779520 8701040 11.162 14.887
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2674334 5.7843 10.8138
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1254082 3.746 6.7429
Pocillopora_meandrina_HIv1___xfSc0000006 290100 834875 2.8779 5.6995
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2518319 9.9831 13.1087
Pocillopora_meandrina_HIv1___xfSc0000012 148278 673146 4.5398 10.7637
Pocillopora_meandrina_HIv1___xfSc0000014 118081 22895 0.1939 0.8024
Pocillopora_meandrina_HIv1___xfSc0000017 98555 550624 5.587 89.0245
Pocillopora_meandrina_HIv1___xfSc0000021 95778 761467 7.9503 14.1705
Pocillopora_meandrina_HIv1___xfSc0000024 90744 655018 7.2183 11.5801
Pocillopora_meandrina_HIv1___xfSc0000029 85532 248011 2.8996 7.816
Pocillopora_meandrina_HIv1___xfSc0000038 77395 51315 0.663 6.518
Pocillopora_meandrina_HIv1___xfSc0000058 69718 561109 8.0483 12.1615
Pocillopora_meandrina_HIv1___xfSc0000059 69426 538690 7.7592 11.4264
Pocillopora_meandrina_HIv1___xfSc0000074 66573 326976 4.9115 8.149
Pocillopora_meandrina_HIv1___xfSc0000081 65415 264799 4.048 6.7745
Pocillopora_meandrina_HIv1___xfSc0000083 65317 954121 14.6075 14.2194
Pocillopora_meandrina_HIv1___xfSc0000092 63607 667300 10.491 12.6045
Pocillopora_meandrina_HIv1___xfSc0000094 62842 113786 1.8107 4.6144
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1318970 21.781 25.6517
Pocillopora_meandrina_HIv1___xfSc0000132 59032 48387 0.8197 2.492
Pocillopora_meandrina_HIv1___xfSc0000145 58221 737048 12.6595 11.0446
Pocillopora_meandrina_HIv1___xfSc0000146 58151 166633 2.8655 7.9131
Pocillopora_meandrina_HIv1___xfSc0000168 56681 381898 6.7377 10.3162
Pocillopora_meandrina_HIv1___xfSc0000175 56271 276086 4.9064 12.4139
Pocillopora_meandrina_HIv1___xfSc0000195 55223 8039 0.1456 1.0418
Pocillopora_meandrina_HIv1___xfSc0000199 55095 978250 17.7557 28.7729
Pocillopora_meandrina_HIv1___xfSc0000205 54658 408271 7.4696 13.2678
Pocillopora_meandrina_HIv1___xfSc0000206 54623 254953 4.6675 7.1951
Pocillopora_meandrina_HIv1___xfSc0000212 54299 403764 7.4359 10.7896
Pocillopora_meandrina_HIv1___xfSc0000217 54168 409846 7.5662 18.9602
Pocillopora_meandrina_HIv1___xfSc0000223 53823 493411 9.1673 10.4317
Pocillopora_meandrina_HIv1___xfSc0000228 53382 604530 11.3246 39.2089
Pocillopora_meandrina_HIv1___xfSc0000237 53049 325952 6.1444 8.9283
Pocillopora_meandrina_HIv1___xfSc0000262 52308 220262 4.2109 6.8065
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1597539 30.5667 28.6941
Pocillopora_meandrina_HIv1___xfSc0000272 52107 398332 7.6445 11.6506
Pocillopora_meandrina_HIv1___xfSc0000275 51938 214596 4.1318 7.5931
Pocillopora_meandrina_HIv1___xfSc0000284 51483 503603 9.7819 11.8554
Pocillopora_meandrina_HIv1___xfSc0000288 51367 969309 18.8703 21.4934
Pocillopora_meandrina_HIv1___xfSc0000300 50845 10481 0.2061 0.7976
Pocillopora_meandrina_HIv1___xfSc0000301 50809 572335 11.2644 11.3355
Pocillopora_meandrina_HIv1___xfSc0000343 49544 214691 4.3333 8.5796
Pocillopora_meandrina_HIv1___xfSc0000376 48519 443857 9.1481 25.6939
Pocillopora_meandrina_HIv1___xfSc0000415 47398 495907 10.4626 12.219
Pocillopora_meandrina_HIv1___xfSc0000423 47202 56123 1.189 3.5727
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1755319 37.2711 41.9642
Pocillopora_meandrina_HIv1___xfSc0000428 47057 520991 11.0715 23.1012
Pocillopora_meandrina_HIv1___xfSc0000436 46816 500426 10.6892 22.5232
Pocillopora_meandrina_HIv1___xfSc0000445 46561 80642 1.732 3.5307
Pocillopora_meandrina_HIv1___xfSc0000447 46542 341494 7.3373 9.7129
Pocillopora_meandrina_HIv1___xfSc0000469 45938 486077 10.5812 10.5819
Pocillopora_meandrina_HIv1___xfSc0000477 45781 570840 12.4689 16.4494
Pocillopora_meandrina_HIv1___xfSc0000479 45736 200922 4.3931 7.2143
Pocillopora_meandrina_HIv1___xfSc0000482 45585 1014508 22.2553 33.9491
Pocillopora_meandrina_HIv1___xfSc0000488 45379 358055 7.8903 11.8142
Pocillopora_meandrina_HIv1___xfSc0000506 44781 229056 5.115 6.9535
Pocillopora_meandrina_HIv1___xfSc0000527 44235 310921 7.0288 10.9662
Pocillopora_meandrina_HIv1___xfSc0000540 43935 373999 8.5126 11.004
Pocillopora_meandrina_HIv1___xfSc0000555 43535 277382 6.3715 11.0014
Pocillopora_meandrina_HIv1___xfSc0000565 43357 434883 10.0303 10.4872
Pocillopora_meandrina_HIv1___xfSc0000566 43316 281143 6.4905 9.4332
Pocillopora_meandrina_HIv1___xfSc0000567 43305 240529 5.5543 10.8014
Pocillopora_meandrina_HIv1___xfSc0000570 43295 131971 3.0482 7.6556
Pocillopora_meandrina_HIv1___xfSc0000579 43029 71644 1.665 3.9928
Pocillopora_meandrina_HIv1___xfSc0000583 42958 401508 9.3465 9.8991
Pocillopora_meandrina_HIv1___xfSc0000596 42675 272484 6.3851 12.0232
Pocillopora_meandrina_HIv1___xfSc0000612 42423 145417 3.4278 5.5854
Pocillopora_meandrina_HIv1___xfSc0000616 42355 3110677 73.443 201.2428
Pocillopora_meandrina_HIv1___xfSc0000621 42164 481680 11.424 13.3008
Pocillopora_meandrina_HIv1___xfSc0000642 41754 169663 4.0634 7.4236
Pocillopora_meandrina_HIv1___xfSc0000655 41446 271956 6.5617 13.377
Pocillopora_meandrina_HIv1___xfSc0000692 40426 473511 11.713 13.1668
Pocillopora_meandrina_HIv1___xfSc0000699 40296 37229 0.9239 2.1683
Pocillopora_meandrina_HIv1___xfSc0000704 40233 667463 16.5899 20.4322
Pocillopora_meandrina_HIv1___xfSc0000705 40197 146024 3.6327 7.3271
Pocillopora_meandrina_HIv1___xfSc0000716 39998 237854 5.9466 9.8564
Pocillopora_meandrina_HIv1___xfSc0000725 39827 109683 2.754 8.1628
Pocillopora_meandrina_HIv1___xfSc0000729 39775 22852 0.5745 4.3729
Pocillopora_meandrina_HIv1___xfSc0000760 39228 7139 0.182 0.9387
Pocillopora_meandrina_HIv1___xfSc0000763 39151 313702 8.0126 7.4382
Pocillopora_meandrina_HIv1___xfSc0000765 39117 127000 3.2467 8.7133
Pocillopora_meandrina_HIv1___xfSc0000788 38513 380157 9.8709 13.4039
Pocillopora_meandrina_HIv1___xfSc0000811 37888 663791 17.5198 16.065
Pocillopora_meandrina_HIv1___xfSc0000812 37881 26908 0.7103 1.4477
Pocillopora_meandrina_HIv1___xfSc0000817 37779 499952 13.2336 11.8984
Pocillopora_meandrina_HIv1___xfSc0000824 37656 295682 7.8522 12.549
Pocillopora_meandrina_HIv1___xfSc0000835 37434 164787 4.4021 6.9176
Pocillopora_meandrina_HIv1___xfSc0000836 37372 254708 6.8155 13.5849
Pocillopora_meandrina_HIv1___xfSc0000837 37368 425262 11.3804 9.8904
Pocillopora_meandrina_HIv1___xfSc0000840 37283 402767 10.803 20.8344
Pocillopora_meandrina_HIv1___xfSc0000857 37006 232660 6.2871 8.5571
Pocillopora_meandrina_HIv1___xfSc0000859 36995 48813 1.3194 3.2659
Pocillopora_meandrina_HIv1___xfSc0000866 36925 83339 2.257 4.1764
Pocillopora_meandrina_HIv1___xfSc0000868 36831 134029 3.639 7.0883
Pocillopora_meandrina_HIv1___xfSc0000875 36611 41613 1.1366 3.2863
Pocillopora_meandrina_HIv1___xfSc0000885 36416 391032 10.7379 15.5146
Pocillopora_meandrina_HIv1___xfSc0000886 36355 210676 5.795 13.0388
Pocillopora_meandrina_HIv1___xfSc0000890 36339 272477 7.4982 10.2791
Pocillopora_meandrina_HIv1___xfSc0000892 36267 205859 5.6762 27.3098
Pocillopora_meandrina_HIv1___xfSc0000943 35168 11897 0.3383 1.3591
Pocillopora_meandrina_HIv1___xfSc0000948 35100 263826 7.5164 11.0005
Pocillopora_meandrina_HIv1___xfSc0000952 34934 117491 3.3632 7.6704
Pocillopora_meandrina_HIv1___xfSc0000953 34905 222875 6.3852 8.1037
Pocillopora_meandrina_HIv1___xfSc0000957 34773 289809 8.3343 14.5666
Pocillopora_meandrina_HIv1___xfSc0000968 34345 17896 0.5211 1.8348
Pocillopora_meandrina_HIv1___xfSc0000974 34140 319205 9.3499 10.2231
Pocillopora_meandrina_HIv1___xfSc0000975 33988 415873 12.2359 11.5224
Pocillopora_meandrina_HIv1___xfSc0000995 33324 127728 3.8329 9.7262
Pocillopora_meandrina_HIv1___xfSc0001011 32918 358048 10.877 23.7467
Pocillopora_meandrina_HIv1___xfSc0001122 29140 530136 18.1927 14.4719
Pocillopora_meandrina_HIv1___xfSc0001170 27381 29950 1.0938 3.0683
Pocillopora_meandrina_HIv1___xfSc0001179 27200 105156 3.866 7.0265
Pocillopora_meandrina_HIv1___xfSc0001231 22938 18619 0.8117 1.4603
Pocillopora_meandrina_HIv1___xfSc0001237 22715 89540 3.9419 9.8762
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3651126 8.9429 14.5309
Pocillopora_meandrina_HIv1___xpSc0001275 48561 205484 4.2315 8.6462
Pocillopora_meandrina_HIv1___xpSc0001276 38618 45049 1.1665 4.0168
Pocillopora_meandrina_HIv1___xpSc0001280 35955 319003 8.8723 11.5108
Pocillopora_meandrina_HIv1___xpSc0001281 34238 237670 6.9417 12.2254
Pocillopora_meandrina_HIv1___xpSc0001290 28931 395614 13.6744 11.9801
Pocillopora_meandrina_HIv1___xpSc0001321 15304 93377 6.1015 10.8429
Pocillopora_meandrina_HIv1___xpSc0001331 8958 142543 15.9124 9.9488
Pocillopora_meandrina_HIv1___xpSc0001337 6786 178386 26.2874 9.8336
Pocillopora_meandrina_HIv1___xpSc0001344 5647 33934 6.0092 7.9019
Pocillopora_meandrina_HIv1___xpSc0001355 3576 59761 16.7117 9.9865

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 01:37:07
    Generated by QualiMap v.2.3