Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-53-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-53-TP2_R1_001.fastp-trim.fq.gz -2 POC-53-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-53-TP2 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:43:31 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-53-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 51,807,794
Mapped reads 51,807,794 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 51,807,794 / 100%
Mapped reads, first in pair 25,903,897 / 50%
Mapped reads, second in pair 25,903,897 / 50%
Mapped reads, both in pair 51,807,794 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.03
Overlapping read pairs 14,108,924 / 54.47%
Duplicated reads (estimated) 6,460,192 / 12.47%
Duplication rate 12.07%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,766,688,437 / 40.32%
Number/percentage of C's 668,467,542 / 9.74%
Number/percentage of T's 2,771,032,079 / 40.38%
Number/percentage of G's 654,809,981 / 9.54%
Number/percentage of N's 571,255 / 0.01%
GC Percentage 19.29%

Coverage

Mean 18.2791
Standard Deviation 17.8573
Mean (paired-end reads overlap ignored) 15.76

Mapping Quality

Mean Mapping Quality 22.61

Insert size

Mean 264.79
Standard Deviation 90.81
P25/Median/P75 193 / 257 / 328

Mismatches and indels

General error rate 21.19%
Mismatches 1,428,332,882
Insertions 10,154,565
Mapped reads with at least one insertion 14.74%
Deletions 8,104,937
Mapped reads with at least one deletion 13.12%
Homopolymer indels 52.2%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 424464138 19.6047 13.8962
Pocillopora_meandrina_HIv1___Sc0000001 21507942 442594110 20.5782 13.2186
Pocillopora_meandrina_HIv1___Sc0000002 19741974 403486247 20.438 13.7861
Pocillopora_meandrina_HIv1___Sc0000003 19417450 353321078 18.1961 15.5267
Pocillopora_meandrina_HIv1___Sc0000004 14584444 253292001 17.3673 20.0935
Pocillopora_meandrina_HIv1___Sc0000005 14098929 277225554 19.6629 13.5643
Pocillopora_meandrina_HIv1___Sc0000006 14068054 274943080 19.5438 14.1955
Pocillopora_meandrina_HIv1___Sc0000007 13590779 258824473 19.0441 15.1793
Pocillopora_meandrina_HIv1___Sc0000008 12446599 256912393 20.6412 14.2881
Pocillopora_meandrina_HIv1___Sc0000009 11983232 121333323 10.1253 14.9914
Pocillopora_meandrina_HIv1___Sc0000010 11763137 218100228 18.541 16.4889
Pocillopora_meandrina_HIv1___Sc0000011 10501528 234881730 22.3664 12.0036
Pocillopora_meandrina_HIv1___Sc0000012 10024633 191572367 19.1102 23.6468
Pocillopora_meandrina_HIv1___Sc0000013 9946974 149257919 15.0054 14.2166
Pocillopora_meandrina_HIv1___Sc0000014 9536826 196914983 20.6479 12.9989
Pocillopora_meandrina_HIv1___Sc0000015 9393205 182200798 19.3971 14.2168
Pocillopora_meandrina_HIv1___Sc0000016 9288165 176243495 18.9751 14.2716
Pocillopora_meandrina_HIv1___Sc0000017 9274345 177567839 19.1461 14.1139
Pocillopora_meandrina_HIv1___Sc0000018 8584156 173937179 20.2626 13.6221
Pocillopora_meandrina_HIv1___Sc0000019 7112774 132143691 18.5784 14.4825
Pocillopora_meandrina_HIv1___Sc0000020 6748058 127408175 18.8807 15.8094
Pocillopora_meandrina_HIv1___Sc0000021 6546105 133365847 20.3733 13.9806
Pocillopora_meandrina_HIv1___Sc0000022 6319256 113241687 17.9201 18.1271
Pocillopora_meandrina_HIv1___Sc0000023 5767069 96266377 16.6924 15.4411
Pocillopora_meandrina_HIv1___Sc0000024 5762297 68674872 11.918 14.2731
Pocillopora_meandrina_HIv1___Sc0000025 5759531 93163716 16.1756 16.2831
Pocillopora_meandrina_HIv1___Sc0000026 5647578 124043954 21.9641 12.3751
Pocillopora_meandrina_HIv1___Sc0000027 5550630 99501980 17.9262 21.6303
Pocillopora_meandrina_HIv1___Sc0000028 5130920 107316800 20.9157 15.8981
Pocillopora_meandrina_HIv1___Sc0000029 4860867 80449470 16.5504 13.5566
Pocillopora_meandrina_HIv1___Sc0000030 4843735 94545802 19.5192 12.1089
Pocillopora_meandrina_HIv1___Sc0000031 4691590 92002056 19.61 13.3868
Pocillopora_meandrina_HIv1___Sc0000032 3615800 76982892 21.2907 14.9091
Pocillopora_meandrina_HIv1___Sc0000033 3306609 48140649 14.5589 13.5529
Pocillopora_meandrina_HIv1___Sc0000034 3122802 61797825 19.7892 13.5451
Pocillopora_meandrina_HIv1___Sc0000035 3015365 48203059 15.9858 15.5716
Pocillopora_meandrina_HIv1___Sc0000036 3007169 68479987 22.7722 12.409
Pocillopora_meandrina_HIv1___Sc0000037 2860435 60761522 21.2421 19.5863
Pocillopora_meandrina_HIv1___Sc0000038 2701138 53818844 19.9245 17.1386
Pocillopora_meandrina_HIv1___Sc0000039 2599273 38659492 14.8732 13.7668
Pocillopora_meandrina_HIv1___Sc0000040 2445666 46367486 18.959 18.467
Pocillopora_meandrina_HIv1___Sc0000041 2159376 42336859 19.6061 12.7321
Pocillopora_meandrina_HIv1___Sc0000042 1957488 30026261 15.3392 13.1312
Pocillopora_meandrina_HIv1___Sc0000043 1845599 29386585 15.9225 13.1275
Pocillopora_meandrina_HIv1___Sc0000044 1724711 34804210 20.1797 13.818
Pocillopora_meandrina_HIv1___Sc0000045 1153740 16151837 13.9995 12.9392
Pocillopora_meandrina_HIv1___Sc0000046 755410 10042834 13.2945 17.336
Pocillopora_meandrina_HIv1___Sc0000047 239089 509090 2.1293 6.9708
Pocillopora_meandrina_HIv1___Sc0000048 214660 61004 0.2842 1.5107
Pocillopora_meandrina_HIv1___Sc0000049 179266 566366 3.1594 9.0284
Pocillopora_meandrina_HIv1___Sc0000050 177168 224084 1.2648 3.4233
Pocillopora_meandrina_HIv1___Sc0000051 165057 947358 5.7396 9.1654
Pocillopora_meandrina_HIv1___Sc0000052 155210 85059 0.548 5.7745
Pocillopora_meandrina_HIv1___Sc0000053 123249 321023 2.6047 6.4319
Pocillopora_meandrina_HIv1___Sc0000054 122643 1869343 15.2421 15.6945
Pocillopora_meandrina_HIv1___Sc0000055 121609 671145 5.5189 11.0876
Pocillopora_meandrina_HIv1___Sc0000056 112816 97747 0.8664 8.7777
Pocillopora_meandrina_HIv1___Sc0000057 107171 467869 4.3656 10.5239
Pocillopora_meandrina_HIv1___Sc0000058 98341 90750 0.9228 9.8552
Pocillopora_meandrina_HIv1___Sc0000059 83292 3764 0.0452 0.2155
Pocillopora_meandrina_HIv1___Sc0000060 79483 503 0.0063 0.1208
Pocillopora_meandrina_HIv1___Sc0000061 75390 252217 3.3455 7.8987
Pocillopora_meandrina_HIv1___Sc0000062 74194 18015 0.2428 1.0509
Pocillopora_meandrina_HIv1___Sc0000063 73457 69496 0.9461 10.139
Pocillopora_meandrina_HIv1___Sc0000064 72700 7272 0.1 0.5884
Pocillopora_meandrina_HIv1___Sc0000065 67986 13445 0.1978 1.3796
Pocillopora_meandrina_HIv1___Sc0000066 66659 555241 8.3296 8.6316
Pocillopora_meandrina_HIv1___Sc0000067 64947 130806 2.014 4.2783
Pocillopora_meandrina_HIv1___Sc0000068 64340 7226 0.1123 0.7369
Pocillopora_meandrina_HIv1___Sc0000069 62616 224167 3.58 8.9079
Pocillopora_meandrina_HIv1___Sc0000070 60121 171005 2.8443 13.3274
Pocillopora_meandrina_HIv1___Sc0000071 57157 73257 1.2817 2.9696
Pocillopora_meandrina_HIv1___Sc0000072 56626 14199 0.2508 2.698
Pocillopora_meandrina_HIv1___Sc0000073 56082 6957 0.1241 0.4693
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 267 0.0049 0.0874
Pocillopora_meandrina_HIv1___Sc0000076 54587 233001 4.2684 21.0227
Pocillopora_meandrina_HIv1___Sc0000077 53379 17989 0.337 0.8285
Pocillopora_meandrina_HIv1___Sc0000078 51564 1826 0.0354 0.3748
Pocillopora_meandrina_HIv1___Sc0000079 49664 1080 0.0217 0.1748
Pocillopora_meandrina_HIv1___Sc0000080 47218 106071 2.2464 5.8251
Pocillopora_meandrina_HIv1___Sc0000081 42490 20186 0.4751 1.53
Pocillopora_meandrina_HIv1___Sc0000082 32657 579660 17.7499 39.1406
Pocillopora_meandrina_HIv1___Sc0000083 27992 4412 0.1576 0.6173
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 13084098 8.1693 12.549
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4347836 3.6301 7.9485
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5839074 7.4906 10.6972
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1724957 3.7309 6.2491
Pocillopora_meandrina_HIv1___xfSc0000004 334777 894608 2.6723 5.2007
Pocillopora_meandrina_HIv1___xfSc0000006 290100 770472 2.6559 5.0721
Pocillopora_meandrina_HIv1___xfSc0000007 252258 3202946 12.6971 18.5113
Pocillopora_meandrina_HIv1___xfSc0000012 148278 611763 4.1258 9.2421
Pocillopora_meandrina_HIv1___xfSc0000014 118081 31306 0.2651 0.9814
Pocillopora_meandrina_HIv1___xfSc0000017 98555 409155 4.1515 61.5371
Pocillopora_meandrina_HIv1___xfSc0000021 95778 720733 7.525 13.4555
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1195064 13.1696 19.5827
Pocillopora_meandrina_HIv1___xfSc0000029 85532 256240 2.9958 7.7197
Pocillopora_meandrina_HIv1___xfSc0000038 77395 19850 0.2565 1.6975
Pocillopora_meandrina_HIv1___xfSc0000058 69718 840492 12.0556 12.2234
Pocillopora_meandrina_HIv1___xfSc0000059 69426 633950 9.1313 11.3158
Pocillopora_meandrina_HIv1___xfSc0000074 66573 449555 6.7528 7.7065
Pocillopora_meandrina_HIv1___xfSc0000081 65415 422858 6.4642 7.5033
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1106427 16.9393 13.351
Pocillopora_meandrina_HIv1___xfSc0000092 63607 844236 13.2727 15.377
Pocillopora_meandrina_HIv1___xfSc0000094 62842 54145 0.8616 2.2828
Pocillopora_meandrina_HIv1___xfSc0000113 60556 697225 11.5137 11.2612
Pocillopora_meandrina_HIv1___xfSc0000132 59032 50669 0.8583 2.0756
Pocillopora_meandrina_HIv1___xfSc0000145 58221 347982 5.9769 6.7485
Pocillopora_meandrina_HIv1___xfSc0000146 58151 187783 3.2292 7.7107
Pocillopora_meandrina_HIv1___xfSc0000168 56681 357057 6.2994 9.6097
Pocillopora_meandrina_HIv1___xfSc0000175 56271 268853 4.7778 12.4138
Pocillopora_meandrina_HIv1___xfSc0000195 55223 11688 0.2117 1.084
Pocillopora_meandrina_HIv1___xfSc0000199 55095 317614 5.7648 11.5057
Pocillopora_meandrina_HIv1___xfSc0000205 54658 302602 5.5363 7.5998
Pocillopora_meandrina_HIv1___xfSc0000206 54623 305352 5.5902 8.6124
Pocillopora_meandrina_HIv1___xfSc0000212 54299 382062 7.0363 9.7436
Pocillopora_meandrina_HIv1___xfSc0000217 54168 584250 10.7859 22.1593
Pocillopora_meandrina_HIv1___xfSc0000223 53823 419169 7.7879 8.5877
Pocillopora_meandrina_HIv1___xfSc0000228 53382 409891 7.6784 32.1513
Pocillopora_meandrina_HIv1___xfSc0000237 53049 316657 5.9691 8.7968
Pocillopora_meandrina_HIv1___xfSc0000262 52308 434823 8.3127 8.0384
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1281032 24.5108 28.0799
Pocillopora_meandrina_HIv1___xfSc0000272 52107 367179 7.0466 10.4006
Pocillopora_meandrina_HIv1___xfSc0000275 51938 460024 8.8572 10.0803
Pocillopora_meandrina_HIv1___xfSc0000284 51483 602475 11.7024 14.0808
Pocillopora_meandrina_HIv1___xfSc0000288 51367 401069 7.8079 14.5391
Pocillopora_meandrina_HIv1___xfSc0000300 50845 10125 0.1991 0.5703
Pocillopora_meandrina_HIv1___xfSc0000301 50809 590833 11.6285 13.6451
Pocillopora_meandrina_HIv1___xfSc0000343 49544 284466 5.7417 7.3882
Pocillopora_meandrina_HIv1___xfSc0000376 48519 589355 12.1469 40.661
Pocillopora_meandrina_HIv1___xfSc0000415 47398 117084 2.4702 3.8754
Pocillopora_meandrina_HIv1___xfSc0000423 47202 57386 1.2158 2.9288
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1126862 23.9269 29.6343
Pocillopora_meandrina_HIv1___xfSc0000428 47057 773087 16.4287 28.1766
Pocillopora_meandrina_HIv1___xfSc0000436 46816 390967 8.3511 16.1739
Pocillopora_meandrina_HIv1___xfSc0000445 46561 166796 3.5823 6.9966
Pocillopora_meandrina_HIv1___xfSc0000447 46542 514878 11.0627 13.0415
Pocillopora_meandrina_HIv1___xfSc0000469 45938 546864 11.9044 10.5617
Pocillopora_meandrina_HIv1___xfSc0000477 45781 387829 8.4714 9.2692
Pocillopora_meandrina_HIv1___xfSc0000479 45736 208248 4.5533 7.6327
Pocillopora_meandrina_HIv1___xfSc0000482 45585 368976 8.0942 13.7212
Pocillopora_meandrina_HIv1___xfSc0000488 45379 283167 6.24 9.3131
Pocillopora_meandrina_HIv1___xfSc0000506 44781 181852 4.0609 6.3489
Pocillopora_meandrina_HIv1___xfSc0000527 44235 280954 6.3514 8.4513
Pocillopora_meandrina_HIv1___xfSc0000540 43935 456057 10.3803 13.5483
Pocillopora_meandrina_HIv1___xfSc0000555 43535 374471 8.6016 17.0696
Pocillopora_meandrina_HIv1___xfSc0000565 43357 671215 15.4811 13.4602
Pocillopora_meandrina_HIv1___xfSc0000566 43316 269859 6.23 9.9529
Pocillopora_meandrina_HIv1___xfSc0000567 43305 221808 5.122 10.566
Pocillopora_meandrina_HIv1___xfSc0000570 43295 96843 2.2368 5.5363
Pocillopora_meandrina_HIv1___xfSc0000579 43029 74375 1.7285 4.2064
Pocillopora_meandrina_HIv1___xfSc0000583 42958 384674 8.9547 9.5865
Pocillopora_meandrina_HIv1___xfSc0000596 42675 222218 5.2072 9.0968
Pocillopora_meandrina_HIv1___xfSc0000612 42423 235071 5.5411 7.4261
Pocillopora_meandrina_HIv1___xfSc0000616 42355 11483758 271.1311 803.1576
Pocillopora_meandrina_HIv1___xfSc0000621 42164 330661 7.8423 9.3494
Pocillopora_meandrina_HIv1___xfSc0000642 41754 224705 5.3816 7.5792
Pocillopora_meandrina_HIv1___xfSc0000655 41446 457960 11.0496 24.4661
Pocillopora_meandrina_HIv1___xfSc0000692 40426 61397 1.5188 5.1359
Pocillopora_meandrina_HIv1___xfSc0000699 40296 42282 1.0493 2.4026
Pocillopora_meandrina_HIv1___xfSc0000704 40233 759690 18.8823 24.5769
Pocillopora_meandrina_HIv1___xfSc0000705 40197 139662 3.4744 6.6257
Pocillopora_meandrina_HIv1___xfSc0000716 39998 354262 8.857 9.7365
Pocillopora_meandrina_HIv1___xfSc0000725 39827 156331 3.9253 12.0824
Pocillopora_meandrina_HIv1___xfSc0000729 39775 17169 0.4317 2.2631
Pocillopora_meandrina_HIv1___xfSc0000760 39228 6100 0.1555 0.5304
Pocillopora_meandrina_HIv1___xfSc0000763 39151 280576 7.1665 7.0074
Pocillopora_meandrina_HIv1___xfSc0000765 39117 96254 2.4607 5.8162
Pocillopora_meandrina_HIv1___xfSc0000788 38513 515824 13.3935 20.0306
Pocillopora_meandrina_HIv1___xfSc0000811 37888 312501 8.248 10.5805
Pocillopora_meandrina_HIv1___xfSc0000812 37881 22108 0.5836 1.4618
Pocillopora_meandrina_HIv1___xfSc0000817 37779 527048 13.9508 9.5584
Pocillopora_meandrina_HIv1___xfSc0000824 37656 49264 1.3083 2.1231
Pocillopora_meandrina_HIv1___xfSc0000835 37434 226413 6.0483 6.8546
Pocillopora_meandrina_HIv1___xfSc0000836 37372 275076 7.3605 11.1903
Pocillopora_meandrina_HIv1___xfSc0000837 37368 123226 3.2976 6.8605
Pocillopora_meandrina_HIv1___xfSc0000840 37283 252087 6.7614 17.5722
Pocillopora_meandrina_HIv1___xfSc0000857 37006 158874 4.2932 5.8673
Pocillopora_meandrina_HIv1___xfSc0000859 36995 58565 1.5831 2.8626
Pocillopora_meandrina_HIv1___xfSc0000866 36925 57847 1.5666 2.931
Pocillopora_meandrina_HIv1___xfSc0000868 36831 113898 3.0924 7.7371
Pocillopora_meandrina_HIv1___xfSc0000875 36611 59986 1.6385 3.9469
Pocillopora_meandrina_HIv1___xfSc0000885 36416 221672 6.0872 8.2867
Pocillopora_meandrina_HIv1___xfSc0000886 36355 220408 6.0627 9.5435
Pocillopora_meandrina_HIv1___xfSc0000890 36339 238639 6.567 11.9832
Pocillopora_meandrina_HIv1___xfSc0000892 36267 108083 2.9802 11.973
Pocillopora_meandrina_HIv1___xfSc0000943 35168 6956 0.1978 0.9822
Pocillopora_meandrina_HIv1___xfSc0000948 35100 248656 7.0842 8.7156
Pocillopora_meandrina_HIv1___xfSc0000952 34934 224318 6.4212 8.4589
Pocillopora_meandrina_HIv1___xfSc0000953 34905 198257 5.6799 6.8895
Pocillopora_meandrina_HIv1___xfSc0000957 34773 298660 8.5888 9.6874
Pocillopora_meandrina_HIv1___xfSc0000968 34345 16089 0.4685 2.1432
Pocillopora_meandrina_HIv1___xfSc0000974 34140 305485 8.948 9.1237
Pocillopora_meandrina_HIv1___xfSc0000975 33988 394418 11.6046 10.7835
Pocillopora_meandrina_HIv1___xfSc0000995 33324 98983 2.9703 6.8724
Pocillopora_meandrina_HIv1___xfSc0001011 32918 164891 5.0091 9.8401
Pocillopora_meandrina_HIv1___xfSc0001122 29140 285146 9.7854 12.5574
Pocillopora_meandrina_HIv1___xfSc0001170 27381 19914 0.7273 2.1404
Pocillopora_meandrina_HIv1___xfSc0001179 27200 105431 3.8761 6.768
Pocillopora_meandrina_HIv1___xfSc0001231 22938 19264 0.8398 1.7744
Pocillopora_meandrina_HIv1___xfSc0001237 22715 108764 4.7882 12.047
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2259919 5.5354 10.9254
Pocillopora_meandrina_HIv1___xpSc0001275 48561 189278 3.8977 7.8329
Pocillopora_meandrina_HIv1___xpSc0001276 38618 66246 1.7154 4.8047
Pocillopora_meandrina_HIv1___xpSc0001280 35955 201936 5.6164 8.3784
Pocillopora_meandrina_HIv1___xpSc0001281 34238 210196 6.1393 8.5182
Pocillopora_meandrina_HIv1___xpSc0001290 28931 333916 11.5418 10.9038
Pocillopora_meandrina_HIv1___xpSc0001321 15304 39724 2.5957 5.3582
Pocillopora_meandrina_HIv1___xpSc0001331 8958 213171 23.7967 10.4075
Pocillopora_meandrina_HIv1___xpSc0001337 6786 28757 4.2377 8.5433
Pocillopora_meandrina_HIv1___xpSc0001344 5647 72007 12.7514 15.7675
Pocillopora_meandrina_HIv1___xpSc0001355 3576 40626 11.3607 10.1324

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 21:43:38
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