Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-53-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-53-TP1_R1_001.fastp-trim.fq.gz -2 POC-53-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-53-TP1 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 01:54:54 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-53-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 52,172,182
Mapped reads 52,172,182 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 52,172,182 / 100%
Mapped reads, first in pair 26,086,091 / 50%
Mapped reads, second in pair 26,086,091 / 50%
Mapped reads, both in pair 52,172,182 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.69
Overlapping read pairs 14,217,306 / 54.5%
Duplicated reads (estimated) 6,539,317 / 12.53%
Duplication rate 12.22%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,780,180,225 / 40.34%
Number/percentage of C's 670,689,706 / 9.73%
Number/percentage of T's 2,783,783,185 / 40.39%
Number/percentage of G's 656,437,279 / 9.53%
Number/percentage of N's 570,489 / 0.01%
GC Percentage 19.26%

Coverage

Mean 18.3596
Standard Deviation 15.9682
Mean (paired-end reads overlap ignored) 15.92

Mapping Quality

Mean Mapping Quality 22.65

Insert size

Mean 264.26
Standard Deviation 89.51
P25/Median/P75 197 / 258 / 324

Mismatches and indels

General error rate 21.15%
Mismatches 1,431,302,662
Insertions 10,302,971
Mapped reads with at least one insertion 14.82%
Deletions 8,205,793
Mapped reads with at least one deletion 13.19%
Homopolymer indels 52.16%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 427503616 19.7451 13.9683
Pocillopora_meandrina_HIv1___Sc0000001 21507942 444518540 20.6676 13.2607
Pocillopora_meandrina_HIv1___Sc0000002 19741974 403030142 20.4149 13.7661
Pocillopora_meandrina_HIv1___Sc0000003 19417450 355469258 18.3067 15.5388
Pocillopora_meandrina_HIv1___Sc0000004 14584444 254976397 17.4828 20.2929
Pocillopora_meandrina_HIv1___Sc0000005 14098929 278957491 19.7857 13.5746
Pocillopora_meandrina_HIv1___Sc0000006 14068054 275576910 19.5888 14.043
Pocillopora_meandrina_HIv1___Sc0000007 13590779 259791256 19.1153 15.2931
Pocillopora_meandrina_HIv1___Sc0000008 12446599 256990120 20.6474 14.3175
Pocillopora_meandrina_HIv1___Sc0000009 11983232 123876461 10.3375 15.251
Pocillopora_meandrina_HIv1___Sc0000010 11763137 218632838 18.5863 16.394
Pocillopora_meandrina_HIv1___Sc0000011 10501528 235427960 22.4184 12.0629
Pocillopora_meandrina_HIv1___Sc0000012 10024633 192063922 19.1592 17.2745
Pocillopora_meandrina_HIv1___Sc0000013 9946974 149450646 15.0247 14.2312
Pocillopora_meandrina_HIv1___Sc0000014 9536826 198864481 20.8523 13.2042
Pocillopora_meandrina_HIv1___Sc0000015 9393205 182830984 19.4642 14.2651
Pocillopora_meandrina_HIv1___Sc0000016 9288165 177336811 19.0928 14.4151
Pocillopora_meandrina_HIv1___Sc0000017 9274345 177717311 19.1622 14.0908
Pocillopora_meandrina_HIv1___Sc0000018 8584156 174212951 20.2947 13.6788
Pocillopora_meandrina_HIv1___Sc0000019 7112774 133421363 18.758 14.6387
Pocillopora_meandrina_HIv1___Sc0000020 6748058 128387429 19.0258 15.7897
Pocillopora_meandrina_HIv1___Sc0000021 6546105 134296750 20.5155 14.1363
Pocillopora_meandrina_HIv1___Sc0000022 6319256 113290765 17.9279 18.0359
Pocillopora_meandrina_HIv1___Sc0000023 5767069 97332189 16.8772 15.5528
Pocillopora_meandrina_HIv1___Sc0000024 5762297 69478226 12.0574 14.4902
Pocillopora_meandrina_HIv1___Sc0000025 5759531 94121094 16.3418 16.569
Pocillopora_meandrina_HIv1___Sc0000026 5647578 124831684 22.1036 12.4271
Pocillopora_meandrina_HIv1___Sc0000027 5550630 100218196 18.0553 21.8828
Pocillopora_meandrina_HIv1___Sc0000028 5130920 108292447 21.1059 16.1128
Pocillopora_meandrina_HIv1___Sc0000029 4860867 81340877 16.7338 13.7241
Pocillopora_meandrina_HIv1___Sc0000030 4843735 95460581 19.7081 12.2974
Pocillopora_meandrina_HIv1___Sc0000031 4691590 92359562 19.6862 13.3533
Pocillopora_meandrina_HIv1___Sc0000032 3615800 77681063 21.4838 14.9497
Pocillopora_meandrina_HIv1___Sc0000033 3306609 48770833 14.7495 13.7465
Pocillopora_meandrina_HIv1___Sc0000034 3122802 62051353 19.8704 13.4719
Pocillopora_meandrina_HIv1___Sc0000035 3015365 48974363 16.2416 15.8752
Pocillopora_meandrina_HIv1___Sc0000036 3007169 68528437 22.7884 12.3767
Pocillopora_meandrina_HIv1___Sc0000037 2860435 61098314 21.3598 19.3954
Pocillopora_meandrina_HIv1___Sc0000038 2701138 53648645 19.8615 17.0338
Pocillopora_meandrina_HIv1___Sc0000039 2599273 38913306 14.9708 13.9932
Pocillopora_meandrina_HIv1___Sc0000040 2445666 47074999 19.2483 18.5808
Pocillopora_meandrina_HIv1___Sc0000041 2159376 42905396 19.8693 12.9289
Pocillopora_meandrina_HIv1___Sc0000042 1957488 30207377 15.4317 13.1245
Pocillopora_meandrina_HIv1___Sc0000043 1845599 29516184 15.9927 13.1904
Pocillopora_meandrina_HIv1___Sc0000044 1724711 34953698 20.2664 13.9556
Pocillopora_meandrina_HIv1___Sc0000045 1153740 16387984 14.2042 13.2373
Pocillopora_meandrina_HIv1___Sc0000046 755410 9931934 13.1477 17.3095
Pocillopora_meandrina_HIv1___Sc0000047 239089 532757 2.2283 7.5103
Pocillopora_meandrina_HIv1___Sc0000048 214660 55417 0.2582 1.5316
Pocillopora_meandrina_HIv1___Sc0000049 179266 560742 3.128 8.9148
Pocillopora_meandrina_HIv1___Sc0000050 177168 192710 1.0877 2.8078
Pocillopora_meandrina_HIv1___Sc0000051 165057 967499 5.8616 9.2822
Pocillopora_meandrina_HIv1___Sc0000052 155210 96123 0.6193 6.6346
Pocillopora_meandrina_HIv1___Sc0000053 123249 350241 2.8417 6.8272
Pocillopora_meandrina_HIv1___Sc0000054 122643 1828364 14.908 15.2435
Pocillopora_meandrina_HIv1___Sc0000055 121609 676189 5.5604 11.2312
Pocillopora_meandrina_HIv1___Sc0000056 112816 78048 0.6918 6.6723
Pocillopora_meandrina_HIv1___Sc0000057 107171 489728 4.5696 10.8521
Pocillopora_meandrina_HIv1___Sc0000058 98341 111186 1.1306 11.8953
Pocillopora_meandrina_HIv1___Sc0000059 83292 3132 0.0376 0.2693
Pocillopora_meandrina_HIv1___Sc0000060 79483 117 0.0015 0.0515
Pocillopora_meandrina_HIv1___Sc0000061 75390 238570 3.1645 7.0767
Pocillopora_meandrina_HIv1___Sc0000062 74194 26212 0.3533 1.5789
Pocillopora_meandrina_HIv1___Sc0000063 73457 63196 0.8603 9.0794
Pocillopora_meandrina_HIv1___Sc0000064 72700 6715 0.0924 0.3703
Pocillopora_meandrina_HIv1___Sc0000065 67986 11235 0.1653 1.4005
Pocillopora_meandrina_HIv1___Sc0000066 66659 583948 8.7602 8.9504
Pocillopora_meandrina_HIv1___Sc0000067 64947 141197 2.174 4.4595
Pocillopora_meandrina_HIv1___Sc0000068 64340 7916 0.123 0.7353
Pocillopora_meandrina_HIv1___Sc0000069 62616 221759 3.5416 8.9357
Pocillopora_meandrina_HIv1___Sc0000070 60121 166570 2.7706 12.9763
Pocillopora_meandrina_HIv1___Sc0000071 57157 75959 1.329 3.3246
Pocillopora_meandrina_HIv1___Sc0000072 56626 15063 0.266 2.8264
Pocillopora_meandrina_HIv1___Sc0000073 56082 9042 0.1612 0.6142
Pocillopora_meandrina_HIv1___Sc0000074 55210 806 0.0146 0.1962
Pocillopora_meandrina_HIv1___Sc0000075 54685 1216 0.0222 0.1596
Pocillopora_meandrina_HIv1___Sc0000076 54587 233654 4.2804 21.171
Pocillopora_meandrina_HIv1___Sc0000077 53379 18988 0.3557 0.8689
Pocillopora_meandrina_HIv1___Sc0000078 51564 811 0.0157 0.202
Pocillopora_meandrina_HIv1___Sc0000079 49664 2764 0.0557 0.2872
Pocillopora_meandrina_HIv1___Sc0000080 47218 106788 2.2616 6.0455
Pocillopora_meandrina_HIv1___Sc0000081 42490 20360 0.4792 1.5074
Pocillopora_meandrina_HIv1___Sc0000082 32657 569608 17.4421 37.4138
Pocillopora_meandrina_HIv1___Sc0000083 27992 3282 0.1172 0.5427
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 13215767 8.2516 12.8669
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4528965 3.7813 8.2683
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5947597 7.6298 10.9856
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1806277 3.9068 6.5755
Pocillopora_meandrina_HIv1___xfSc0000004 334777 909104 2.7156 5.2222
Pocillopora_meandrina_HIv1___xfSc0000006 290100 756046 2.6062 4.9929
Pocillopora_meandrina_HIv1___xfSc0000007 252258 3255781 12.9066 18.6799
Pocillopora_meandrina_HIv1___xfSc0000012 148278 623636 4.2059 9.5034
Pocillopora_meandrina_HIv1___xfSc0000014 118081 28445 0.2409 0.846
Pocillopora_meandrina_HIv1___xfSc0000017 98555 395391 4.0119 58.8925
Pocillopora_meandrina_HIv1___xfSc0000021 95778 720098 7.5184 13.7257
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1193600 13.1535 19.3285
Pocillopora_meandrina_HIv1___xfSc0000029 85532 246409 2.8809 7.9432
Pocillopora_meandrina_HIv1___xfSc0000038 77395 20478 0.2646 1.7195
Pocillopora_meandrina_HIv1___xfSc0000058 69718 861009 12.3499 12.6291
Pocillopora_meandrina_HIv1___xfSc0000059 69426 605301 8.7187 10.4124
Pocillopora_meandrina_HIv1___xfSc0000074 66573 435751 6.5455 7.4403
Pocillopora_meandrina_HIv1___xfSc0000081 65415 447667 6.8435 7.8334
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1168670 17.8923 14.2073
Pocillopora_meandrina_HIv1___xfSc0000092 63607 823891 12.9528 14.2331
Pocillopora_meandrina_HIv1___xfSc0000094 62842 63169 1.0052 2.5027
Pocillopora_meandrina_HIv1___xfSc0000113 60556 667872 11.029 10.5033
Pocillopora_meandrina_HIv1___xfSc0000132 59032 49238 0.8341 2.173
Pocillopora_meandrina_HIv1___xfSc0000145 58221 351008 6.0289 6.9126
Pocillopora_meandrina_HIv1___xfSc0000146 58151 189361 3.2564 8.0879
Pocillopora_meandrina_HIv1___xfSc0000168 56681 353968 6.2449 9.3977
Pocillopora_meandrina_HIv1___xfSc0000175 56271 286939 5.0992 13.0969
Pocillopora_meandrina_HIv1___xfSc0000195 55223 14554 0.2635 1.4555
Pocillopora_meandrina_HIv1___xfSc0000199 55095 331753 6.0215 11.6507
Pocillopora_meandrina_HIv1___xfSc0000205 54658 316835 5.7967 8.02
Pocillopora_meandrina_HIv1___xfSc0000206 54623 307017 5.6207 8.8882
Pocillopora_meandrina_HIv1___xfSc0000212 54299 385304 7.096 10.0838
Pocillopora_meandrina_HIv1___xfSc0000217 54168 577765 10.6662 21.4894
Pocillopora_meandrina_HIv1___xfSc0000223 53823 438278 8.143 9.1122
Pocillopora_meandrina_HIv1___xfSc0000228 53382 415284 7.7795 33.1418
Pocillopora_meandrina_HIv1___xfSc0000237 53049 310848 5.8596 8.5624
Pocillopora_meandrina_HIv1___xfSc0000262 52308 459323 8.7811 8.9123
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1312123 25.1057 29.2647
Pocillopora_meandrina_HIv1___xfSc0000272 52107 353470 6.7835 9.7862
Pocillopora_meandrina_HIv1___xfSc0000275 51938 452189 8.7063 10.1584
Pocillopora_meandrina_HIv1___xfSc0000284 51483 568820 11.0487 13.8653
Pocillopora_meandrina_HIv1___xfSc0000288 51367 392057 7.6325 14.9859
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9295 0.1828 0.696
Pocillopora_meandrina_HIv1___xfSc0000301 50809 605770 11.9225 14.8834
Pocillopora_meandrina_HIv1___xfSc0000343 49544 287667 5.8063 8.0223
Pocillopora_meandrina_HIv1___xfSc0000376 48519 587160 12.1017 39.6359
Pocillopora_meandrina_HIv1___xfSc0000415 47398 133607 2.8188 4.4701
Pocillopora_meandrina_HIv1___xfSc0000423 47202 54941 1.164 3.2308
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1101886 23.3966 29.7111
Pocillopora_meandrina_HIv1___xfSc0000428 47057 833934 17.7218 30.4971
Pocillopora_meandrina_HIv1___xfSc0000436 46816 436226 9.3179 18.4834
Pocillopora_meandrina_HIv1___xfSc0000445 46561 168511 3.6191 6.692
Pocillopora_meandrina_HIv1___xfSc0000447 46542 522821 11.2333 13.0302
Pocillopora_meandrina_HIv1___xfSc0000469 45938 555030 12.0822 10.5186
Pocillopora_meandrina_HIv1___xfSc0000477 45781 396257 8.6555 8.8775
Pocillopora_meandrina_HIv1___xfSc0000479 45736 187876 4.1078 6.64
Pocillopora_meandrina_HIv1___xfSc0000482 45585 342407 7.5114 12.7496
Pocillopora_meandrina_HIv1___xfSc0000488 45379 292863 6.4537 9.7989
Pocillopora_meandrina_HIv1___xfSc0000506 44781 177202 3.9571 5.813
Pocillopora_meandrina_HIv1___xfSc0000527 44235 297817 6.7326 9.417
Pocillopora_meandrina_HIv1___xfSc0000540 43935 474307 10.7957 14.6606
Pocillopora_meandrina_HIv1___xfSc0000555 43535 381588 8.7651 17.4472
Pocillopora_meandrina_HIv1___xfSc0000565 43357 658880 15.1966 13.3234
Pocillopora_meandrina_HIv1___xfSc0000566 43316 258637 5.9709 9.2805
Pocillopora_meandrina_HIv1___xfSc0000567 43305 203054 4.6889 10.464
Pocillopora_meandrina_HIv1___xfSc0000570 43295 90903 2.0996 4.9806
Pocillopora_meandrina_HIv1___xfSc0000579 43029 73987 1.7195 4.3872
Pocillopora_meandrina_HIv1___xfSc0000583 42958 361209 8.4084 9.2948
Pocillopora_meandrina_HIv1___xfSc0000596 42675 218621 5.1229 8.5605
Pocillopora_meandrina_HIv1___xfSc0000612 42423 225967 5.3265 7.4758
Pocillopora_meandrina_HIv1___xfSc0000616 42355 5448692 128.6434 416.5281
Pocillopora_meandrina_HIv1___xfSc0000621 42164 353837 8.3919 10.2143
Pocillopora_meandrina_HIv1___xfSc0000642 41754 221227 5.2983 7.2714
Pocillopora_meandrina_HIv1___xfSc0000655 41446 471836 11.3844 24.9435
Pocillopora_meandrina_HIv1___xfSc0000692 40426 64559 1.597 5.5641
Pocillopora_meandrina_HIv1___xfSc0000699 40296 42041 1.0433 2.6679
Pocillopora_meandrina_HIv1___xfSc0000704 40233 766401 19.0491 24.121
Pocillopora_meandrina_HIv1___xfSc0000705 40197 144024 3.583 6.9139
Pocillopora_meandrina_HIv1___xfSc0000716 39998 356823 8.921 9.8273
Pocillopora_meandrina_HIv1___xfSc0000725 39827 156884 3.9391 12.0326
Pocillopora_meandrina_HIv1___xfSc0000729 39775 13928 0.3502 2.0266
Pocillopora_meandrina_HIv1___xfSc0000760 39228 4542 0.1158 0.6432
Pocillopora_meandrina_HIv1___xfSc0000763 39151 297369 7.5954 7.8339
Pocillopora_meandrina_HIv1___xfSc0000765 39117 106019 2.7103 6.6765
Pocillopora_meandrina_HIv1___xfSc0000788 38513 520019 13.5024 19.378
Pocillopora_meandrina_HIv1___xfSc0000811 37888 315233 8.3201 10.3653
Pocillopora_meandrina_HIv1___xfSc0000812 37881 22332 0.5895 1.3158
Pocillopora_meandrina_HIv1___xfSc0000817 37779 530681 14.047 9.6383
Pocillopora_meandrina_HIv1___xfSc0000824 37656 50378 1.3378 2.414
Pocillopora_meandrina_HIv1___xfSc0000835 37434 242904 6.4889 7.5777
Pocillopora_meandrina_HIv1___xfSc0000836 37372 259612 6.9467 10.4839
Pocillopora_meandrina_HIv1___xfSc0000837 37368 113584 3.0396 6.0733
Pocillopora_meandrina_HIv1___xfSc0000840 37283 233416 6.2607 16.8588
Pocillopora_meandrina_HIv1___xfSc0000857 37006 148831 4.0218 5.4435
Pocillopora_meandrina_HIv1___xfSc0000859 36995 67311 1.8195 3.0663
Pocillopora_meandrina_HIv1___xfSc0000866 36925 66388 1.7979 3.5566
Pocillopora_meandrina_HIv1___xfSc0000868 36831 115504 3.1361 9.2262
Pocillopora_meandrina_HIv1___xfSc0000875 36611 63623 1.7378 4.3556
Pocillopora_meandrina_HIv1___xfSc0000885 36416 218082 5.9886 7.9248
Pocillopora_meandrina_HIv1___xfSc0000886 36355 206990 5.6936 9.0698
Pocillopora_meandrina_HIv1___xfSc0000890 36339 229256 6.3088 13.3722
Pocillopora_meandrina_HIv1___xfSc0000892 36267 109922 3.0309 12.4926
Pocillopora_meandrina_HIv1___xfSc0000943 35168 7207 0.2049 0.9612
Pocillopora_meandrina_HIv1___xfSc0000948 35100 247337 7.0466 8.7272
Pocillopora_meandrina_HIv1___xfSc0000952 34934 224986 6.4403 8.6804
Pocillopora_meandrina_HIv1___xfSc0000953 34905 197883 5.6692 6.9801
Pocillopora_meandrina_HIv1___xfSc0000957 34773 315770 9.0809 10.2383
Pocillopora_meandrina_HIv1___xfSc0000968 34345 15228 0.4434 1.7483
Pocillopora_meandrina_HIv1___xfSc0000974 34140 300500 8.802 9.5766
Pocillopora_meandrina_HIv1___xfSc0000975 33988 372484 10.9593 10.4025
Pocillopora_meandrina_HIv1___xfSc0000995 33324 101462 3.0447 7.0814
Pocillopora_meandrina_HIv1___xfSc0001011 32918 168220 5.1103 9.7609
Pocillopora_meandrina_HIv1___xfSc0001122 29140 307953 10.5681 13.119
Pocillopora_meandrina_HIv1___xfSc0001170 27381 24343 0.889 2.4781
Pocillopora_meandrina_HIv1___xfSc0001179 27200 109245 4.0164 6.8276
Pocillopora_meandrina_HIv1___xfSc0001231 22938 22235 0.9694 1.729
Pocillopora_meandrina_HIv1___xfSc0001237 22715 135561 5.9679 15.7489
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2246169 5.5017 10.7328
Pocillopora_meandrina_HIv1___xpSc0001275 48561 192898 3.9723 8.3975
Pocillopora_meandrina_HIv1___xpSc0001276 38618 66248 1.7155 5.4685
Pocillopora_meandrina_HIv1___xpSc0001280 35955 197136 5.4829 8.1997
Pocillopora_meandrina_HIv1___xpSc0001281 34238 218028 6.368 9.1279
Pocillopora_meandrina_HIv1___xpSc0001290 28931 324231 11.207 11.0462
Pocillopora_meandrina_HIv1___xpSc0001321 15304 39311 2.5687 4.5311
Pocillopora_meandrina_HIv1___xpSc0001331 8958 210327 23.4792 10.4555
Pocillopora_meandrina_HIv1___xpSc0001337 6786 25820 3.8049 6.7891
Pocillopora_meandrina_HIv1___xpSc0001344 5647 85096 15.0692 18.6835
Pocillopora_meandrina_HIv1___xpSc0001355 3576 43335 12.1183 10.5884

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 01:54:59
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