Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-222-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-222-TP1_R1_001.fastp-trim.fq.gz -2 POC-222-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-222-TP1 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:49:43 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-222-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 50,878,076
Mapped reads 50,878,076 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 50,878,076 / 100%
Mapped reads, first in pair 25,439,038 / 50%
Mapped reads, second in pair 25,439,038 / 50%
Mapped reads, both in pair 50,878,076 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.98
Overlapping read pairs 14,178,088 / 55.73%
Duplicated reads (estimated) 5,991,283 / 11.78%
Duplication rate 11.51%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,718,776,320 / 40.37%
Number/percentage of C's 655,204,402 / 9.73%
Number/percentage of T's 2,719,396,970 / 40.38%
Number/percentage of G's 641,324,621 / 9.52%
Number/percentage of N's 542,510 / 0.01%
GC Percentage 19.25%

Coverage

Mean 17.9429
Standard Deviation 16.2015
Mean (paired-end reads overlap ignored) 15.56

Mapping Quality

Mean Mapping Quality 22.8

Insert size

Mean 262.32
Standard Deviation 86.24
P25/Median/P75 199 / 256 / 318

Mismatches and indels

General error rate 21.12%
Mismatches 1,396,422,571
Insertions 10,118,109
Mapped reads with at least one insertion 14.89%
Deletions 8,017,403
Mapped reads with at least one deletion 13.21%
Homopolymer indels 52.25%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 415701563 19.2 13.6657
Pocillopora_meandrina_HIv1___Sc0000001 21507942 432217624 20.0957 12.9089
Pocillopora_meandrina_HIv1___Sc0000002 19741974 392748109 19.8941 13.3704
Pocillopora_meandrina_HIv1___Sc0000003 19417450 327010505 16.8411 14.3697
Pocillopora_meandrina_HIv1___Sc0000004 14584444 259041171 17.7615 23.3583
Pocillopora_meandrina_HIv1___Sc0000005 14098929 273135546 19.3728 12.8287
Pocillopora_meandrina_HIv1___Sc0000006 14068054 272058077 19.3387 15.08
Pocillopora_meandrina_HIv1___Sc0000007 13590779 262387705 19.3063 15.122
Pocillopora_meandrina_HIv1___Sc0000008 12446599 252842251 20.3142 14.1155
Pocillopora_meandrina_HIv1___Sc0000009 11983232 122309310 10.2067 16.2025
Pocillopora_meandrina_HIv1___Sc0000010 11763137 206655394 17.5681 16.4216
Pocillopora_meandrina_HIv1___Sc0000011 10501528 233968052 22.2794 12.9388
Pocillopora_meandrina_HIv1___Sc0000012 10024633 188947470 18.8483 19.6804
Pocillopora_meandrina_HIv1___Sc0000013 9946974 144881276 14.5654 14.0794
Pocillopora_meandrina_HIv1___Sc0000014 9536826 194172611 20.3603 13.2437
Pocillopora_meandrina_HIv1___Sc0000015 9393205 171795415 18.2893 13.2249
Pocillopora_meandrina_HIv1___Sc0000016 9288165 172158349 18.5352 14.2635
Pocillopora_meandrina_HIv1___Sc0000017 9274345 170936858 18.4312 13.3123
Pocillopora_meandrina_HIv1___Sc0000018 8584156 167075325 19.4632 13.0511
Pocillopora_meandrina_HIv1___Sc0000019 7112774 130061062 18.2856 14.2949
Pocillopora_meandrina_HIv1___Sc0000020 6748058 122651630 18.1758 13.4499
Pocillopora_meandrina_HIv1___Sc0000021 6546105 130423961 19.9239 13.8598
Pocillopora_meandrina_HIv1___Sc0000022 6319256 109565289 17.3383 17.154
Pocillopora_meandrina_HIv1___Sc0000023 5767069 91128708 15.8016 14.284
Pocillopora_meandrina_HIv1___Sc0000024 5762297 69440159 12.0508 17.5072
Pocillopora_meandrina_HIv1___Sc0000025 5759531 96263143 16.7137 17.5244
Pocillopora_meandrina_HIv1___Sc0000026 5647578 124696076 22.0796 12.6604
Pocillopora_meandrina_HIv1___Sc0000027 5550630 103297928 18.6101 21.9495
Pocillopora_meandrina_HIv1___Sc0000028 5130920 110377676 21.5123 18.8371
Pocillopora_meandrina_HIv1___Sc0000029 4860867 74275605 15.2803 13.2406
Pocillopora_meandrina_HIv1___Sc0000030 4843735 97423271 20.1133 12.2214
Pocillopora_meandrina_HIv1___Sc0000031 4691590 92541318 19.7249 13.3971
Pocillopora_meandrina_HIv1___Sc0000032 3615800 76883014 21.2631 14.5675
Pocillopora_meandrina_HIv1___Sc0000033 3306609 47517563 14.3705 13.3271
Pocillopora_meandrina_HIv1___Sc0000034 3122802 63238509 20.2506 14.5726
Pocillopora_meandrina_HIv1___Sc0000035 3015365 46364780 15.3762 15.1891
Pocillopora_meandrina_HIv1___Sc0000036 3007169 69782600 23.2054 13.2117
Pocillopora_meandrina_HIv1___Sc0000037 2860435 55220390 19.3049 23.9043
Pocillopora_meandrina_HIv1___Sc0000038 2701138 47748546 17.6772 14.0221
Pocillopora_meandrina_HIv1___Sc0000039 2599273 36737236 14.1337 13.9454
Pocillopora_meandrina_HIv1___Sc0000040 2445666 45962526 18.7935 17.3456
Pocillopora_meandrina_HIv1___Sc0000041 2159376 44622117 20.6644 12.5535
Pocillopora_meandrina_HIv1___Sc0000042 1957488 31749669 16.2196 13.5186
Pocillopora_meandrina_HIv1___Sc0000043 1845599 28090661 15.2203 12.8797
Pocillopora_meandrina_HIv1___Sc0000044 1724711 35002316 20.2946 15.0601
Pocillopora_meandrina_HIv1___Sc0000045 1153740 19434098 16.8444 15.078
Pocillopora_meandrina_HIv1___Sc0000046 755410 9925891 13.1397 18.1741
Pocillopora_meandrina_HIv1___Sc0000047 239089 149542 0.6255 2.2683
Pocillopora_meandrina_HIv1___Sc0000048 214660 56938 0.2652 1.805
Pocillopora_meandrina_HIv1___Sc0000049 179266 945488 5.2742 11.5395
Pocillopora_meandrina_HIv1___Sc0000050 177168 247428 1.3966 3.2642
Pocillopora_meandrina_HIv1___Sc0000051 165057 847400 5.134 9.3921
Pocillopora_meandrina_HIv1___Sc0000052 155210 121582 0.7833 8.2471
Pocillopora_meandrina_HIv1___Sc0000053 123249 363572 2.9499 7.0947
Pocillopora_meandrina_HIv1___Sc0000054 122643 1820055 14.8403 15.6223
Pocillopora_meandrina_HIv1___Sc0000055 121609 640615 5.2678 10.9338
Pocillopora_meandrina_HIv1___Sc0000056 112816 92746 0.8221 8.1331
Pocillopora_meandrina_HIv1___Sc0000057 107171 326659 3.048 7.4257
Pocillopora_meandrina_HIv1___Sc0000058 98341 103097 1.0484 9.6938
Pocillopora_meandrina_HIv1___Sc0000059 83292 9367 0.1125 0.4932
Pocillopora_meandrina_HIv1___Sc0000060 79483 796 0.01 0.1687
Pocillopora_meandrina_HIv1___Sc0000061 75390 276192 3.6635 7.5775
Pocillopora_meandrina_HIv1___Sc0000062 74194 24592 0.3315 1.5253
Pocillopora_meandrina_HIv1___Sc0000063 73457 100122 1.363 12.9948
Pocillopora_meandrina_HIv1___Sc0000064 72700 18233 0.2508 1.2484
Pocillopora_meandrina_HIv1___Sc0000065 67986 2152 0.0317 0.2754
Pocillopora_meandrina_HIv1___Sc0000066 66659 538681 8.0811 8.567
Pocillopora_meandrina_HIv1___Sc0000067 64947 145863 2.2459 4.7321
Pocillopora_meandrina_HIv1___Sc0000068 64340 8231 0.1279 0.8221
Pocillopora_meandrina_HIv1___Sc0000069 62616 227833 3.6386 9.3884
Pocillopora_meandrina_HIv1___Sc0000070 60121 360157 5.9905 32.4458
Pocillopora_meandrina_HIv1___Sc0000071 57157 51271 0.897 2.1017
Pocillopora_meandrina_HIv1___Sc0000072 56626 13081 0.231 2.3734
Pocillopora_meandrina_HIv1___Sc0000073 56082 16172 0.2884 0.9263
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 538 0.0098 0.1362
Pocillopora_meandrina_HIv1___Sc0000076 54587 210875 3.8631 19.2006
Pocillopora_meandrina_HIv1___Sc0000077 53379 40052 0.7503 2.04
Pocillopora_meandrina_HIv1___Sc0000078 51564 148 0.0029 0.0718
Pocillopora_meandrina_HIv1___Sc0000079 49664 1342 0.027 0.1742
Pocillopora_meandrina_HIv1___Sc0000080 47218 106497 2.2554 4.9886
Pocillopora_meandrina_HIv1___Sc0000081 42490 18839 0.4434 1.5733
Pocillopora_meandrina_HIv1___Sc0000082 32657 679074 20.7941 45.9919
Pocillopora_meandrina_HIv1___Sc0000083 27992 2959 0.1057 0.4697
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 8591945 5.3646 9.1236
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4953569 4.1358 8.6606
Pocillopora_meandrina_HIv1___xfSc0000002 779520 11435376 14.6698 19.7936
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1101560 2.3825 5.1364
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1729366 5.1657 8.5851
Pocillopora_meandrina_HIv1___xfSc0000006 290100 443073 1.5273 4.1056
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1940760 7.6936 10.376
Pocillopora_meandrina_HIv1___xfSc0000012 148278 801414 5.4048 9.1571
Pocillopora_meandrina_HIv1___xfSc0000014 118081 24125 0.2043 0.9184
Pocillopora_meandrina_HIv1___xfSc0000017 98555 544929 5.5292 79.9072
Pocillopora_meandrina_HIv1___xfSc0000021 95778 653166 6.8196 11.4833
Pocillopora_meandrina_HIv1___xfSc0000024 90744 651509 7.1796 10.0102
Pocillopora_meandrina_HIv1___xfSc0000029 85532 109749 1.2831 4.9269
Pocillopora_meandrina_HIv1___xfSc0000038 77395 94596 1.2222 14.8142
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1138021 16.3232 18.0759
Pocillopora_meandrina_HIv1___xfSc0000059 69426 383885 5.5294 10.3124
Pocillopora_meandrina_HIv1___xfSc0000074 66573 327724 4.9228 8.0444
Pocillopora_meandrina_HIv1___xfSc0000081 65415 433201 6.6223 7.5497
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1002120 15.3424 15.8044
Pocillopora_meandrina_HIv1___xfSc0000092 63607 532000 8.3639 9.7532
Pocillopora_meandrina_HIv1___xfSc0000094 62842 136032 2.1647 5.0373
Pocillopora_meandrina_HIv1___xfSc0000113 60556 952866 15.7353 17.4284
Pocillopora_meandrina_HIv1___xfSc0000132 59032 38287 0.6486 1.7118
Pocillopora_meandrina_HIv1___xfSc0000145 58221 654832 11.2474 9.6344
Pocillopora_meandrina_HIv1___xfSc0000146 58151 187068 3.2169 6.9139
Pocillopora_meandrina_HIv1___xfSc0000168 56681 380150 6.7068 10.0149
Pocillopora_meandrina_HIv1___xfSc0000175 56271 232260 4.1275 10.0761
Pocillopora_meandrina_HIv1___xfSc0000195 55223 19441 0.352 2.3967
Pocillopora_meandrina_HIv1___xfSc0000199 55095 261733 4.7506 7.4322
Pocillopora_meandrina_HIv1___xfSc0000205 54658 144847 2.6501 4.8336
Pocillopora_meandrina_HIv1___xfSc0000206 54623 260566 4.7703 7.4903
Pocillopora_meandrina_HIv1___xfSc0000212 54299 408076 7.5154 11.0112
Pocillopora_meandrina_HIv1___xfSc0000217 54168 417482 7.7072 15.9083
Pocillopora_meandrina_HIv1___xfSc0000223 53823 572954 10.6452 9.8666
Pocillopora_meandrina_HIv1___xfSc0000228 53382 308211 5.7737 27.1866
Pocillopora_meandrina_HIv1___xfSc0000237 53049 316871 5.9732 8.4304
Pocillopora_meandrina_HIv1___xfSc0000262 52308 238842 4.5661 6.3262
Pocillopora_meandrina_HIv1___xfSc0000264 52264 840901 16.0895 13.5809
Pocillopora_meandrina_HIv1___xfSc0000272 52107 509865 9.785 13.7277
Pocillopora_meandrina_HIv1___xfSc0000275 51938 605179 11.652 15.9166
Pocillopora_meandrina_HIv1___xfSc0000284 51483 570285 11.0772 13.2774
Pocillopora_meandrina_HIv1___xfSc0000288 51367 389576 7.5842 15.7619
Pocillopora_meandrina_HIv1___xfSc0000300 50845 14672 0.2886 0.9579
Pocillopora_meandrina_HIv1___xfSc0000301 50809 682547 13.4336 11.3766
Pocillopora_meandrina_HIv1___xfSc0000343 49544 337143 6.8049 11.1369
Pocillopora_meandrina_HIv1___xfSc0000376 48519 559489 11.5313 36.5032
Pocillopora_meandrina_HIv1___xfSc0000415 47398 296280 6.2509 8.7101
Pocillopora_meandrina_HIv1___xfSc0000423 47202 63553 1.3464 3.6011
Pocillopora_meandrina_HIv1___xfSc0000426 47096 2490934 52.8906 64.0477
Pocillopora_meandrina_HIv1___xfSc0000428 47057 757311 16.0935 22.5768
Pocillopora_meandrina_HIv1___xfSc0000436 46816 334859 7.1527 12.1032
Pocillopora_meandrina_HIv1___xfSc0000445 46561 73051 1.5689 3.8037
Pocillopora_meandrina_HIv1___xfSc0000447 46542 541753 11.6401 11.9867
Pocillopora_meandrina_HIv1___xfSc0000469 45938 607469 13.2237 10.3646
Pocillopora_meandrina_HIv1___xfSc0000477 45781 452781 9.8902 9.3285
Pocillopora_meandrina_HIv1___xfSc0000479 45736 184866 4.042 6.7472
Pocillopora_meandrina_HIv1___xfSc0000482 45585 303197 6.6512 13.0692
Pocillopora_meandrina_HIv1___xfSc0000488 45379 373404 8.2286 11.3042
Pocillopora_meandrina_HIv1___xfSc0000506 44781 194518 4.3438 6.5019
Pocillopora_meandrina_HIv1___xfSc0000527 44235 274601 6.2078 9.3753
Pocillopora_meandrina_HIv1___xfSc0000540 43935 393612 8.959 11.5277
Pocillopora_meandrina_HIv1___xfSc0000555 43535 119451 2.7438 6.7771
Pocillopora_meandrina_HIv1___xfSc0000565 43357 657618 15.1675 12.9863
Pocillopora_meandrina_HIv1___xfSc0000566 43316 359439 8.2981 16.9892
Pocillopora_meandrina_HIv1___xfSc0000567 43305 244999 5.6575 10.1595
Pocillopora_meandrina_HIv1___xfSc0000570 43295 135873 3.1383 8.3654
Pocillopora_meandrina_HIv1___xfSc0000579 43029 98989 2.3005 5.0158
Pocillopora_meandrina_HIv1___xfSc0000583 42958 375742 8.7467 9.0308
Pocillopora_meandrina_HIv1___xfSc0000596 42675 909300 21.3076 10.9904
Pocillopora_meandrina_HIv1___xfSc0000612 42423 216856 5.1118 8.3848
Pocillopora_meandrina_HIv1___xfSc0000616 42355 6769072 159.8175 416.5561
Pocillopora_meandrina_HIv1___xfSc0000621 42164 472257 11.2005 13.6149
Pocillopora_meandrina_HIv1___xfSc0000642 41754 211323 5.0611 7.8436
Pocillopora_meandrina_HIv1___xfSc0000655 41446 601244 14.5067 28.3154
Pocillopora_meandrina_HIv1___xfSc0000692 40426 260278 6.4384 7.5027
Pocillopora_meandrina_HIv1___xfSc0000699 40296 65217 1.6184 3.7952
Pocillopora_meandrina_HIv1___xfSc0000704 40233 749380 18.626 24.5021
Pocillopora_meandrina_HIv1___xfSc0000705 40197 129511 3.2219 6.7653
Pocillopora_meandrina_HIv1___xfSc0000716 39998 286338 7.1588 9.0159
Pocillopora_meandrina_HIv1___xfSc0000725 39827 113782 2.8569 9.248
Pocillopora_meandrina_HIv1___xfSc0000729 39775 71159 1.789 11.7329
Pocillopora_meandrina_HIv1___xfSc0000760 39228 12490 0.3184 1.6012
Pocillopora_meandrina_HIv1___xfSc0000763 39151 303512 7.7523 7.7921
Pocillopora_meandrina_HIv1___xfSc0000765 39117 78554 2.0082 4.7466
Pocillopora_meandrina_HIv1___xfSc0000788 38513 325953 8.4635 13.4818
Pocillopora_meandrina_HIv1___xfSc0000811 37888 223391 5.8961 8.2843
Pocillopora_meandrina_HIv1___xfSc0000812 37881 35712 0.9427 1.4057
Pocillopora_meandrina_HIv1___xfSc0000817 37779 616306 16.3135 7.5861
Pocillopora_meandrina_HIv1___xfSc0000824 37656 104201 2.7672 4.623
Pocillopora_meandrina_HIv1___xfSc0000835 37434 400968 10.7113 12.1221
Pocillopora_meandrina_HIv1___xfSc0000836 37372 279916 7.49 12.013
Pocillopora_meandrina_HIv1___xfSc0000837 37368 233142 6.2391 8.2031
Pocillopora_meandrina_HIv1___xfSc0000840 37283 184293 4.9431 11.1191
Pocillopora_meandrina_HIv1___xfSc0000857 37006 183303 4.9533 5.6521
Pocillopora_meandrina_HIv1___xfSc0000859 36995 33838 0.9147 1.8456
Pocillopora_meandrina_HIv1___xfSc0000866 36925 66826 1.8098 3.7432
Pocillopora_meandrina_HIv1___xfSc0000868 36831 115786 3.1437 7.454
Pocillopora_meandrina_HIv1___xfSc0000875 36611 53826 1.4702 3.7542
Pocillopora_meandrina_HIv1___xfSc0000885 36416 182570 5.0135 6.5704
Pocillopora_meandrina_HIv1___xfSc0000886 36355 99660 2.7413 5.0527
Pocillopora_meandrina_HIv1___xfSc0000890 36339 229212 6.3076 8.9317
Pocillopora_meandrina_HIv1___xfSc0000892 36267 272562 7.5154 36.2601
Pocillopora_meandrina_HIv1___xfSc0000943 35168 5671 0.1613 0.6454
Pocillopora_meandrina_HIv1___xfSc0000948 35100 253820 7.2313 9.8276
Pocillopora_meandrina_HIv1___xfSc0000952 34934 423369 12.1191 6.7262
Pocillopora_meandrina_HIv1___xfSc0000953 34905 223887 6.4142 8.0547
Pocillopora_meandrina_HIv1___xfSc0000957 34773 291592 8.3856 14.5669
Pocillopora_meandrina_HIv1___xfSc0000968 34345 14346 0.4177 1.6644
Pocillopora_meandrina_HIv1___xfSc0000974 34140 299349 8.7683 10.3941
Pocillopora_meandrina_HIv1___xfSc0000975 33988 289411 8.5151 8.4536
Pocillopora_meandrina_HIv1___xfSc0000995 33324 102369 3.0719 8.2123
Pocillopora_meandrina_HIv1___xfSc0001011 32918 184050 5.5912 12.308
Pocillopora_meandrina_HIv1___xfSc0001122 29140 413307 14.1835 12.677
Pocillopora_meandrina_HIv1___xfSc0001170 27381 20396 0.7449 1.8516
Pocillopora_meandrina_HIv1___xfSc0001179 27200 115391 4.2423 7.0787
Pocillopora_meandrina_HIv1___xfSc0001231 22938 24321 1.0603 1.7606
Pocillopora_meandrina_HIv1___xfSc0001237 22715 25792 1.1355 3.3888
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2840650 6.9578 12.1386
Pocillopora_meandrina_HIv1___xpSc0001275 48561 256790 5.288 9.3416
Pocillopora_meandrina_HIv1___xpSc0001276 38618 112721 2.9189 6.1161
Pocillopora_meandrina_HIv1___xpSc0001280 35955 93054 2.5881 4.2597
Pocillopora_meandrina_HIv1___xpSc0001281 34238 182905 5.3422 7.8809
Pocillopora_meandrina_HIv1___xpSc0001290 28931 204893 7.0821 7.7094
Pocillopora_meandrina_HIv1___xpSc0001321 15304 36296 2.3717 4.5225
Pocillopora_meandrina_HIv1___xpSc0001331 8958 181458 20.2565 10.5644
Pocillopora_meandrina_HIv1___xpSc0001337 6786 22076 3.2532 6.9767
Pocillopora_meandrina_HIv1___xpSc0001344 5647 67577 11.9669 14.5168
Pocillopora_meandrina_HIv1___xpSc0001355 3576 58792 16.4407 12.653

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 20:49:48
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