Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-255-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-255-TP1_R1_001.fastp-trim.fq.gz -2 POC-255-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-255-TP1 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:31:05 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-255-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 43,125,754
Mapped reads 43,125,754 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 43,125,754 / 100%
Mapped reads, first in pair 21,562,877 / 50%
Mapped reads, second in pair 21,562,877 / 50%
Mapped reads, both in pair 43,125,754 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.88
Overlapping read pairs 12,006,615 / 55.68%
Duplicated reads (estimated) 4,802,365 / 11.14%
Duplication rate 10.69%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,300,300,952 / 40.33%
Number/percentage of C's 553,745,577 / 9.71%
Number/percentage of T's 2,301,312,293 / 40.35%
Number/percentage of G's 548,024,449 / 9.61%
Number/percentage of N's 471,794 / 0.01%
GC Percentage 19.32%

Coverage

Mean 15.1951
Standard Deviation 14.5557
Mean (paired-end reads overlap ignored) 13.15

Mapping Quality

Mean Mapping Quality 22.47

Insert size

Mean 261.67
Standard Deviation 86.64
P25/Median/P75 197 / 256 / 318

Mismatches and indels

General error rate 21.19%
Mismatches 1,185,677,673
Insertions 8,847,359
Mapped reads with at least one insertion 15.12%
Deletions 6,831,303
Mapped reads with at least one deletion 13.25%
Homopolymer indels 52.24%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 362204605 16.7291 12.4422
Pocillopora_meandrina_HIv1___Sc0000001 21507942 367902047 17.1054 11.4358
Pocillopora_meandrina_HIv1___Sc0000002 19741974 336690929 17.0546 11.8606
Pocillopora_meandrina_HIv1___Sc0000003 19417450 290755404 14.9739 12.9762
Pocillopora_meandrina_HIv1___Sc0000004 14584444 215326764 14.7641 19.8061
Pocillopora_meandrina_HIv1___Sc0000005 14098929 228828295 16.2302 11.3351
Pocillopora_meandrina_HIv1___Sc0000006 14068054 226533708 16.1027 11.9631
Pocillopora_meandrina_HIv1___Sc0000007 13590779 216305911 15.9156 12.552
Pocillopora_meandrina_HIv1___Sc0000008 12446599 213466064 17.1506 11.8223
Pocillopora_meandrina_HIv1___Sc0000009 11983232 109912000 9.1721 13.7545
Pocillopora_meandrina_HIv1___Sc0000010 11763137 178197593 15.1488 15.6221
Pocillopora_meandrina_HIv1___Sc0000011 10501528 194563080 18.5271 10.1776
Pocillopora_meandrina_HIv1___Sc0000012 10024633 157478355 15.7091 16.501
Pocillopora_meandrina_HIv1___Sc0000013 9946974 113884465 11.4492 11.6476
Pocillopora_meandrina_HIv1___Sc0000014 9536826 164383168 17.2367 11.5451
Pocillopora_meandrina_HIv1___Sc0000015 9393205 145471421 15.4869 11.3401
Pocillopora_meandrina_HIv1___Sc0000016 9288165 143984490 15.5019 12.3988
Pocillopora_meandrina_HIv1___Sc0000017 9274345 147939915 15.9515 11.6945
Pocillopora_meandrina_HIv1___Sc0000018 8584156 142951128 16.6529 11.7044
Pocillopora_meandrina_HIv1___Sc0000019 7112774 114515214 16.0999 12.9407
Pocillopora_meandrina_HIv1___Sc0000020 6748058 110280924 16.3426 14.0319
Pocillopora_meandrina_HIv1___Sc0000021 6546105 110334382 16.855 11.6034
Pocillopora_meandrina_HIv1___Sc0000022 6319256 94539741 14.9606 16.5044
Pocillopora_meandrina_HIv1___Sc0000023 5767069 80079610 13.8857 13.0906
Pocillopora_meandrina_HIv1___Sc0000024 5762297 62354889 10.8212 13.0305
Pocillopora_meandrina_HIv1___Sc0000025 5759531 75155873 13.049 12.7053
Pocillopora_meandrina_HIv1___Sc0000026 5647578 106151310 18.7959 14.0061
Pocillopora_meandrina_HIv1___Sc0000027 5550630 71963830 12.965 13.5514
Pocillopora_meandrina_HIv1___Sc0000028 5130920 91127991 17.7606 13.4639
Pocillopora_meandrina_HIv1___Sc0000029 4860867 71663573 14.743 14.5265
Pocillopora_meandrina_HIv1___Sc0000030 4843735 80697111 16.6601 10.8245
Pocillopora_meandrina_HIv1___Sc0000031 4691590 77172247 16.4491 12.8433
Pocillopora_meandrina_HIv1___Sc0000032 3615800 61579730 17.0307 11.5611
Pocillopora_meandrina_HIv1___Sc0000033 3306609 41670254 12.6021 13.2056
Pocillopora_meandrina_HIv1___Sc0000034 3122802 52134271 16.6947 11.8876
Pocillopora_meandrina_HIv1___Sc0000035 3015365 36861248 12.2245 12.776
Pocillopora_meandrina_HIv1___Sc0000036 3007169 53587958 17.8201 10.2317
Pocillopora_meandrina_HIv1___Sc0000037 2860435 44107786 15.42 16.884
Pocillopora_meandrina_HIv1___Sc0000038 2701138 40408472 14.9598 13.4891
Pocillopora_meandrina_HIv1___Sc0000039 2599273 32190967 12.3846 21.6788
Pocillopora_meandrina_HIv1___Sc0000040 2445666 41857006 17.1148 17.6124
Pocillopora_meandrina_HIv1___Sc0000041 2159376 38537496 17.8466 11.3865
Pocillopora_meandrina_HIv1___Sc0000042 1957488 25750989 13.1551 11.8017
Pocillopora_meandrina_HIv1___Sc0000043 1845599 24809211 13.4424 11.1921
Pocillopora_meandrina_HIv1___Sc0000044 1724711 27810761 16.1249 13.5519
Pocillopora_meandrina_HIv1___Sc0000045 1153740 16346652 14.1684 12.611
Pocillopora_meandrina_HIv1___Sc0000046 755410 7533781 9.9731 13.8644
Pocillopora_meandrina_HIv1___Sc0000047 239089 423190 1.77 4.7625
Pocillopora_meandrina_HIv1___Sc0000048 214660 47251 0.2201 1.4179
Pocillopora_meandrina_HIv1___Sc0000049 179266 683791 3.8144 7.1741
Pocillopora_meandrina_HIv1___Sc0000050 177168 221896 1.2525 3.3958
Pocillopora_meandrina_HIv1___Sc0000051 165057 829777 5.0272 9.0312
Pocillopora_meandrina_HIv1___Sc0000052 155210 162940 1.0498 12.5859
Pocillopora_meandrina_HIv1___Sc0000053 123249 351201 2.8495 6.2041
Pocillopora_meandrina_HIv1___Sc0000054 122643 1414282 11.5317 12.2408
Pocillopora_meandrina_HIv1___Sc0000055 121609 603566 4.9632 11.5121
Pocillopora_meandrina_HIv1___Sc0000056 112816 69301 0.6143 5.506
Pocillopora_meandrina_HIv1___Sc0000057 107171 292816 2.7322 7.0848
Pocillopora_meandrina_HIv1___Sc0000058 98341 87249 0.8872 7.0617
Pocillopora_meandrina_HIv1___Sc0000059 83292 6393 0.0768 0.4911
Pocillopora_meandrina_HIv1___Sc0000060 79483 264 0.0033 0.0792
Pocillopora_meandrina_HIv1___Sc0000061 75390 217731 2.8881 7.0042
Pocillopora_meandrina_HIv1___Sc0000062 74194 19413 0.2617 0.9317
Pocillopora_meandrina_HIv1___Sc0000063 73457 28023 0.3815 3.4553
Pocillopora_meandrina_HIv1___Sc0000064 72700 3683 0.0507 0.2834
Pocillopora_meandrina_HIv1___Sc0000065 67986 2715 0.0399 0.2888
Pocillopora_meandrina_HIv1___Sc0000066 66659 456291 6.8452 7.1811
Pocillopora_meandrina_HIv1___Sc0000067 64947 115010 1.7708 3.5946
Pocillopora_meandrina_HIv1___Sc0000068 64340 6273 0.0975 0.6091
Pocillopora_meandrina_HIv1___Sc0000069 62616 198936 3.1771 7.9499
Pocillopora_meandrina_HIv1___Sc0000070 60121 336564 5.5981 31.6372
Pocillopora_meandrina_HIv1___Sc0000071 57157 66132 1.157 2.3495
Pocillopora_meandrina_HIv1___Sc0000072 56626 11571 0.2043 1.9543
Pocillopora_meandrina_HIv1___Sc0000073 56082 8032 0.1432 0.4771
Pocillopora_meandrina_HIv1___Sc0000074 55210 269 0.0049 0.0934
Pocillopora_meandrina_HIv1___Sc0000075 54685 799 0.0146 0.2063
Pocillopora_meandrina_HIv1___Sc0000076 54587 240229 4.4008 21.3142
Pocillopora_meandrina_HIv1___Sc0000077 53379 20945 0.3924 0.97
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1079 0.0217 0.1641
Pocillopora_meandrina_HIv1___Sc0000080 47218 78253 1.6573 3.7807
Pocillopora_meandrina_HIv1___Sc0000081 42490 21461 0.5051 1.9489
Pocillopora_meandrina_HIv1___Sc0000082 32657 570003 17.4542 39.1584
Pocillopora_meandrina_HIv1___Sc0000083 27992 2338 0.0835 0.4099
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 11623683 7.2575 12.4011
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4801817 4.0091 8.4397
Pocillopora_meandrina_HIv1___xfSc0000002 779520 6774509 8.6906 11.9883
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1349435 2.9187 5.7268
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1058812 3.1627 5.7068
Pocillopora_meandrina_HIv1___xfSc0000006 290100 518039 1.7857 4.1938
Pocillopora_meandrina_HIv1___xfSc0000007 252258 699671 2.7736 5.1328
Pocillopora_meandrina_HIv1___xfSc0000012 148278 450046 3.0352 5.5745
Pocillopora_meandrina_HIv1___xfSc0000014 118081 21924 0.1857 0.7342
Pocillopora_meandrina_HIv1___xfSc0000017 98555 406433 4.1239 60.761
Pocillopora_meandrina_HIv1___xfSc0000021 95778 391940 4.0922 8.5096
Pocillopora_meandrina_HIv1___xfSc0000024 90744 985025 10.855 14.4495
Pocillopora_meandrina_HIv1___xfSc0000029 85532 191555 2.2396 5.6696
Pocillopora_meandrina_HIv1___xfSc0000038 77395 21222 0.2742 1.7361
Pocillopora_meandrina_HIv1___xfSc0000058 69718 756357 10.8488 11.2893
Pocillopora_meandrina_HIv1___xfSc0000059 69426 423436 6.0991 10.2386
Pocillopora_meandrina_HIv1___xfSc0000074 66573 234841 3.5276 5.9874
Pocillopora_meandrina_HIv1___xfSc0000081 65415 216494 3.3095 5.6529
Pocillopora_meandrina_HIv1___xfSc0000083 65317 952041 14.5757 15.8657
Pocillopora_meandrina_HIv1___xfSc0000092 63607 551077 8.6638 8.9712
Pocillopora_meandrina_HIv1___xfSc0000094 62842 139025 2.2123 4.7859
Pocillopora_meandrina_HIv1___xfSc0000113 60556 836508 13.8138 15.0098
Pocillopora_meandrina_HIv1___xfSc0000132 59032 43077 0.7297 2.0986
Pocillopora_meandrina_HIv1___xfSc0000145 58221 349905 6.0099 6.5402
Pocillopora_meandrina_HIv1___xfSc0000146 58151 184135 3.1665 6.8015
Pocillopora_meandrina_HIv1___xfSc0000168 56681 293497 5.178 7.6997
Pocillopora_meandrina_HIv1___xfSc0000175 56271 226022 4.0167 10.75
Pocillopora_meandrina_HIv1___xfSc0000195 55223 6966 0.1261 0.8301
Pocillopora_meandrina_HIv1___xfSc0000199 55095 288933 5.2443 9.9927
Pocillopora_meandrina_HIv1___xfSc0000205 54658 324233 5.932 12.7459
Pocillopora_meandrina_HIv1___xfSc0000206 54623 214255 3.9224 6.146
Pocillopora_meandrina_HIv1___xfSc0000212 54299 313546 5.7744 8.7156
Pocillopora_meandrina_HIv1___xfSc0000217 54168 285965 5.2792 10.4089
Pocillopora_meandrina_HIv1___xfSc0000223 53823 298050 5.5376 7.5342
Pocillopora_meandrina_HIv1___xfSc0000228 53382 492458 9.2252 24.6581
Pocillopora_meandrina_HIv1___xfSc0000237 53049 230646 4.3478 6.585
Pocillopora_meandrina_HIv1___xfSc0000262 52308 193139 3.6923 5.3801
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1551035 29.6769 24.9387
Pocillopora_meandrina_HIv1___xfSc0000272 52107 354921 6.8114 8.9607
Pocillopora_meandrina_HIv1___xfSc0000275 51938 377707 7.2723 9.9682
Pocillopora_meandrina_HIv1___xfSc0000284 51483 534068 10.3737 13.3452
Pocillopora_meandrina_HIv1___xfSc0000288 51367 624881 12.165 9.8991
Pocillopora_meandrina_HIv1___xfSc0000300 50845 7696 0.1514 0.5704
Pocillopora_meandrina_HIv1___xfSc0000301 50809 429292 8.4491 10.639
Pocillopora_meandrina_HIv1___xfSc0000343 49544 141476 2.8556 5.4011
Pocillopora_meandrina_HIv1___xfSc0000376 48519 293814 6.0556 16.4832
Pocillopora_meandrina_HIv1___xfSc0000415 47398 187607 3.9581 5.2098
Pocillopora_meandrina_HIv1___xfSc0000423 47202 44775 0.9486 2.3561
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1602293 34.0218 34.25
Pocillopora_meandrina_HIv1___xfSc0000428 47057 365658 7.7705 14.1167
Pocillopora_meandrina_HIv1___xfSc0000436 46816 301630 6.4429 10.1096
Pocillopora_meandrina_HIv1___xfSc0000445 46561 52441 1.1263 3.4073
Pocillopora_meandrina_HIv1___xfSc0000447 46542 188091 4.0413 6.3738
Pocillopora_meandrina_HIv1___xfSc0000469 45938 421550 9.1765 8.7729
Pocillopora_meandrina_HIv1___xfSc0000477 45781 172942 3.7776 5.6883
Pocillopora_meandrina_HIv1___xfSc0000479 45736 172004 3.7608 6.1336
Pocillopora_meandrina_HIv1___xfSc0000482 45585 646959 14.1924 22.1906
Pocillopora_meandrina_HIv1___xfSc0000488 45379 236015 5.201 8.6857
Pocillopora_meandrina_HIv1___xfSc0000506 44781 123211 2.7514 4.7434
Pocillopora_meandrina_HIv1___xfSc0000527 44235 210408 4.7566 6.5298
Pocillopora_meandrina_HIv1___xfSc0000540 43935 303534 6.9087 8.3583
Pocillopora_meandrina_HIv1___xfSc0000555 43535 158255 3.6351 6.8693
Pocillopora_meandrina_HIv1___xfSc0000565 43357 545342 12.5779 11.162
Pocillopora_meandrina_HIv1___xfSc0000566 43316 214471 4.9513 7.2329
Pocillopora_meandrina_HIv1___xfSc0000567 43305 183545 4.2384 8.4353
Pocillopora_meandrina_HIv1___xfSc0000570 43295 78917 1.8228 4.666
Pocillopora_meandrina_HIv1___xfSc0000579 43029 70129 1.6298 3.8946
Pocillopora_meandrina_HIv1___xfSc0000583 42958 289296 6.7344 7.4004
Pocillopora_meandrina_HIv1___xfSc0000596 42675 273423 6.4071 10.6541
Pocillopora_meandrina_HIv1___xfSc0000612 42423 120391 2.8379 5.2811
Pocillopora_meandrina_HIv1___xfSc0000616 42355 6505302 153.5899 515.0156
Pocillopora_meandrina_HIv1___xfSc0000621 42164 457389 10.8479 12.8063
Pocillopora_meandrina_HIv1___xfSc0000642 41754 325224 7.7891 10.4205
Pocillopora_meandrina_HIv1___xfSc0000655 41446 179730 4.3365 9.3236
Pocillopora_meandrina_HIv1___xfSc0000692 40426 137291 3.3961 5.5018
Pocillopora_meandrina_HIv1___xfSc0000699 40296 15207 0.3774 1.0528
Pocillopora_meandrina_HIv1___xfSc0000704 40233 528995 13.1483 17.8096
Pocillopora_meandrina_HIv1___xfSc0000705 40197 131694 3.2762 6.2437
Pocillopora_meandrina_HIv1___xfSc0000716 39998 236597 5.9152 6.3947
Pocillopora_meandrina_HIv1___xfSc0000725 39827 128283 3.221 10.4178
Pocillopora_meandrina_HIv1___xfSc0000729 39775 13968 0.3512 2.3836
Pocillopora_meandrina_HIv1___xfSc0000760 39228 8377 0.2135 1.471
Pocillopora_meandrina_HIv1___xfSc0000763 39151 208935 5.3366 5.6332
Pocillopora_meandrina_HIv1___xfSc0000765 39117 76856 1.9648 4.3265
Pocillopora_meandrina_HIv1___xfSc0000788 38513 476360 12.3688 15.4105
Pocillopora_meandrina_HIv1___xfSc0000811 37888 362339 9.5634 9.811
Pocillopora_meandrina_HIv1___xfSc0000812 37881 18623 0.4916 1.1277
Pocillopora_meandrina_HIv1___xfSc0000817 37779 436794 11.5618 9.7062
Pocillopora_meandrina_HIv1___xfSc0000824 37656 106313 2.8233 5.374
Pocillopora_meandrina_HIv1___xfSc0000835 37434 140271 3.7472 6.2224
Pocillopora_meandrina_HIv1___xfSc0000836 37372 218455 5.8454 8.6549
Pocillopora_meandrina_HIv1___xfSc0000837 37368 414016 11.0794 7.3108
Pocillopora_meandrina_HIv1___xfSc0000840 37283 248463 6.6642 9.9137
Pocillopora_meandrina_HIv1___xfSc0000857 37006 102102 2.7591 4.9595
Pocillopora_meandrina_HIv1___xfSc0000859 36995 51811 1.4005 2.4654
Pocillopora_meandrina_HIv1___xfSc0000866 36925 57660 1.5615 4.2065
Pocillopora_meandrina_HIv1___xfSc0000868 36831 114101 3.098 9.1926
Pocillopora_meandrina_HIv1___xfSc0000875 36611 107081 2.9248 7.3088
Pocillopora_meandrina_HIv1___xfSc0000885 36416 154993 4.2562 5.945
Pocillopora_meandrina_HIv1___xfSc0000886 36355 195539 5.3786 9.8171
Pocillopora_meandrina_HIv1___xfSc0000890 36339 194184 5.3437 6.9925
Pocillopora_meandrina_HIv1___xfSc0000892 36267 241162 6.6496 33.2087
Pocillopora_meandrina_HIv1___xfSc0000943 35168 10645 0.3027 1.2571
Pocillopora_meandrina_HIv1___xfSc0000948 35100 220265 6.2754 8.1429
Pocillopora_meandrina_HIv1___xfSc0000952 34934 87897 2.5161 5.7334
Pocillopora_meandrina_HIv1___xfSc0000953 34905 166456 4.7688 6.109
Pocillopora_meandrina_HIv1___xfSc0000957 34773 142010 4.0839 7.4734
Pocillopora_meandrina_HIv1___xfSc0000968 34345 14948 0.4352 1.6936
Pocillopora_meandrina_HIv1___xfSc0000974 34140 243233 7.1246 7.8482
Pocillopora_meandrina_HIv1___xfSc0000975 33988 341940 10.0606 9.7489
Pocillopora_meandrina_HIv1___xfSc0000995 33324 72870 2.1867 5.3395
Pocillopora_meandrina_HIv1___xfSc0001011 32918 159197 4.8362 8.1391
Pocillopora_meandrina_HIv1___xfSc0001122 29140 170241 5.8422 6.703
Pocillopora_meandrina_HIv1___xfSc0001170 27381 15006 0.548 1.3169
Pocillopora_meandrina_HIv1___xfSc0001179 27200 86335 3.1741 5.9754
Pocillopora_meandrina_HIv1___xfSc0001231 22938 14921 0.6505 1.295
Pocillopora_meandrina_HIv1___xfSc0001237 22715 99575 4.3837 12.2394
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2418324 5.9233 11.8455
Pocillopora_meandrina_HIv1___xpSc0001275 48561 233400 4.8063 10.7669
Pocillopora_meandrina_HIv1___xpSc0001276 38618 101738 2.6345 5.7831
Pocillopora_meandrina_HIv1___xpSc0001280 35955 197527 5.4937 8.1324
Pocillopora_meandrina_HIv1___xpSc0001281 34238 235008 6.864 13.0124
Pocillopora_meandrina_HIv1___xpSc0001290 28931 198307 6.8545 7.5339
Pocillopora_meandrina_HIv1___xpSc0001321 15304 53305 3.4831 5.3435
Pocillopora_meandrina_HIv1___xpSc0001331 8958 167932 18.7466 8.9409
Pocillopora_meandrina_HIv1___xpSc0001337 6786 8175 1.2047 2.6414
Pocillopora_meandrina_HIv1___xpSc0001344 5647 44632 7.9037 9.5693
Pocillopora_meandrina_HIv1___xpSc0001355 3576 37888 10.5951 9.5682

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 20:31:06
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