Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-42-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-42-TP2_R1_001.fastp-trim.fq.gz -2 POC-42-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-42-TP2 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 22:43:56 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-42-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 54,779,772
Mapped reads 54,779,772 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 54,779,772 / 100%
Mapped reads, first in pair 27,389,886 / 50%
Mapped reads, second in pair 27,389,886 / 50%
Mapped reads, both in pair 54,779,772 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.1
Overlapping read pairs 14,500,275 / 52.94%
Duplicated reads (estimated) 6,821,258 / 12.45%
Duplication rate 12.29%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,929,434,148 / 40.36%
Number/percentage of C's 704,971,374 / 9.71%
Number/percentage of T's 2,933,525,245 / 40.41%
Number/percentage of G's 690,606,956 / 9.51%
Number/percentage of N's 599,335 / 0.01%
GC Percentage 19.23%

Coverage

Mean 19.3384
Standard Deviation 16.2147
Mean (paired-end reads overlap ignored) 16.85

Mapping Quality

Mean Mapping Quality 22.78

Insert size

Mean 267.61
Standard Deviation 89.11
P25/Median/P75 200 / 261 / 328

Mismatches and indels

General error rate 21.12%
Mismatches 1,506,276,468
Insertions 10,649,106
Mapped reads with at least one insertion 14.68%
Deletions 8,587,306
Mapped reads with at least one deletion 13.15%
Homopolymer indels 52.21%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 452672645 20.9076 14.5963
Pocillopora_meandrina_HIv1___Sc0000001 21507942 467789267 21.7496 14.0945
Pocillopora_meandrina_HIv1___Sc0000002 19741974 424886378 21.522 14.4687
Pocillopora_meandrina_HIv1___Sc0000003 19417450 365911921 18.8445 16.2603
Pocillopora_meandrina_HIv1___Sc0000004 14584444 287512406 19.7136 24.561
Pocillopora_meandrina_HIv1___Sc0000005 14098929 296532204 21.0323 13.615
Pocillopora_meandrina_HIv1___Sc0000006 14068054 288483016 20.5062 14.732
Pocillopora_meandrina_HIv1___Sc0000007 13590779 283442626 20.8555 15.7705
Pocillopora_meandrina_HIv1___Sc0000008 12446599 275181568 22.109 15.0812
Pocillopora_meandrina_HIv1___Sc0000009 11983232 132156660 11.0285 17.4146
Pocillopora_meandrina_HIv1___Sc0000010 11763137 225080119 19.1344 16.8103
Pocillopora_meandrina_HIv1___Sc0000011 10501528 248838747 23.6955 12.7114
Pocillopora_meandrina_HIv1___Sc0000012 10024633 198199607 19.7713 17.0058
Pocillopora_meandrina_HIv1___Sc0000013 9946974 153292420 15.411 14.7616
Pocillopora_meandrina_HIv1___Sc0000014 9536826 205622947 21.5609 14.1993
Pocillopora_meandrina_HIv1___Sc0000015 9393205 188168207 20.0324 14.4206
Pocillopora_meandrina_HIv1___Sc0000016 9288165 188437265 20.2879 15.2586
Pocillopora_meandrina_HIv1___Sc0000017 9274345 185068983 19.9549 14.2981
Pocillopora_meandrina_HIv1___Sc0000018 8584156 179871206 20.9539 14.1628
Pocillopora_meandrina_HIv1___Sc0000019 7112774 141492646 19.8928 15.7586
Pocillopora_meandrina_HIv1___Sc0000020 6748058 133414267 19.7708 14.9129
Pocillopora_meandrina_HIv1___Sc0000021 6546105 141242608 21.5766 14.0177
Pocillopora_meandrina_HIv1___Sc0000022 6319256 124070579 19.6337 19.8284
Pocillopora_meandrina_HIv1___Sc0000023 5767069 101049498 17.5218 15.4278
Pocillopora_meandrina_HIv1___Sc0000024 5762297 80032885 13.8891 17.1559
Pocillopora_meandrina_HIv1___Sc0000025 5759531 93747592 16.2769 15.7694
Pocillopora_meandrina_HIv1___Sc0000026 5647578 134602035 23.8336 13.093
Pocillopora_meandrina_HIv1___Sc0000027 5550630 103699519 18.6825 19.4473
Pocillopora_meandrina_HIv1___Sc0000028 5130920 110455692 21.5275 14.9473
Pocillopora_meandrina_HIv1___Sc0000029 4860867 95238480 19.5929 15.0581
Pocillopora_meandrina_HIv1___Sc0000030 4843735 103313108 21.3292 12.937
Pocillopora_meandrina_HIv1___Sc0000031 4691590 101097317 21.5486 15.1732
Pocillopora_meandrina_HIv1___Sc0000032 3615800 79122992 21.8826 14.7169
Pocillopora_meandrina_HIv1___Sc0000033 3306609 49956876 15.1082 14.989
Pocillopora_meandrina_HIv1___Sc0000034 3122802 66998725 21.4547 14.9962
Pocillopora_meandrina_HIv1___Sc0000035 3015365 50609299 16.7838 16.0547
Pocillopora_meandrina_HIv1___Sc0000036 3007169 70888111 23.573 12.7366
Pocillopora_meandrina_HIv1___Sc0000037 2860435 58967620 20.6149 18.6195
Pocillopora_meandrina_HIv1___Sc0000038 2701138 54277420 20.0943 16.1993
Pocillopora_meandrina_HIv1___Sc0000039 2599273 39835600 15.3257 14.1738
Pocillopora_meandrina_HIv1___Sc0000040 2445666 40002605 16.3565 15.9087
Pocillopora_meandrina_HIv1___Sc0000041 2159376 45821858 21.22 13.4076
Pocillopora_meandrina_HIv1___Sc0000042 1957488 35316314 18.0417 14.2591
Pocillopora_meandrina_HIv1___Sc0000043 1845599 24909834 13.4969 12.0012
Pocillopora_meandrina_HIv1___Sc0000044 1724711 36642583 21.2456 14.1876
Pocillopora_meandrina_HIv1___Sc0000045 1153740 20207463 17.5147 15.435
Pocillopora_meandrina_HIv1___Sc0000046 755410 10389610 13.7536 18.454
Pocillopora_meandrina_HIv1___Sc0000047 239089 591516 2.474 7.1135
Pocillopora_meandrina_HIv1___Sc0000048 214660 54701 0.2548 1.5946
Pocillopora_meandrina_HIv1___Sc0000049 179266 591025 3.2969 9.8502
Pocillopora_meandrina_HIv1___Sc0000050 177168 243049 1.3719 3.8362
Pocillopora_meandrina_HIv1___Sc0000051 165057 774399 4.6917 9.7995
Pocillopora_meandrina_HIv1___Sc0000052 155210 48663 0.3135 3.1312
Pocillopora_meandrina_HIv1___Sc0000053 123249 387835 3.1468 7.5325
Pocillopora_meandrina_HIv1___Sc0000054 122643 1997133 16.2841 16.2817
Pocillopora_meandrina_HIv1___Sc0000055 121609 765628 6.2958 13.9278
Pocillopora_meandrina_HIv1___Sc0000056 112816 76299 0.6763 7.5884
Pocillopora_meandrina_HIv1___Sc0000057 107171 457604 4.2698 8.45
Pocillopora_meandrina_HIv1___Sc0000058 98341 57836 0.5881 5.8424
Pocillopora_meandrina_HIv1___Sc0000059 83292 5820 0.0699 0.3858
Pocillopora_meandrina_HIv1___Sc0000060 79483 795 0.01 0.1083
Pocillopora_meandrina_HIv1___Sc0000061 75390 646837 8.5799 30.9267
Pocillopora_meandrina_HIv1___Sc0000062 74194 15532 0.2093 0.8386
Pocillopora_meandrina_HIv1___Sc0000063 73457 55384 0.754 7.5838
Pocillopora_meandrina_HIv1___Sc0000064 72700 15837 0.2178 0.9718
Pocillopora_meandrina_HIv1___Sc0000065 67986 13193 0.1941 1.9392
Pocillopora_meandrina_HIv1___Sc0000066 66659 597625 8.9654 9.3447
Pocillopora_meandrina_HIv1___Sc0000067 64947 160461 2.4706 5.0822
Pocillopora_meandrina_HIv1___Sc0000068 64340 12857 0.1998 1.0827
Pocillopora_meandrina_HIv1___Sc0000069 62616 228309 3.6462 9.2729
Pocillopora_meandrina_HIv1___Sc0000070 60121 63003 1.0479 4.1797
Pocillopora_meandrina_HIv1___Sc0000071 57157 86571 1.5146 2.9145
Pocillopora_meandrina_HIv1___Sc0000072 56626 14769 0.2608 2.8228
Pocillopora_meandrina_HIv1___Sc0000073 56082 9201 0.1641 0.5656
Pocillopora_meandrina_HIv1___Sc0000074 55210 752 0.0136 0.1492
Pocillopora_meandrina_HIv1___Sc0000075 54685 1596 0.0292 0.2761
Pocillopora_meandrina_HIv1___Sc0000076 54587 230196 4.217 21.3643
Pocillopora_meandrina_HIv1___Sc0000077 53379 31858 0.5968 1.3163
Pocillopora_meandrina_HIv1___Sc0000078 51564 1345 0.0261 0.2449
Pocillopora_meandrina_HIv1___Sc0000079 49664 1689 0.034 0.3386
Pocillopora_meandrina_HIv1___Sc0000080 47218 103811 2.1985 5.8125
Pocillopora_meandrina_HIv1___Sc0000081 42490 10022 0.2359 0.6089
Pocillopora_meandrina_HIv1___Sc0000082 32657 615533 18.8484 40.4162
Pocillopora_meandrina_HIv1___Sc0000083 27992 4751 0.1697 0.7449
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 12959365 8.0915 13.4912
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4082736 3.4088 7.0468
Pocillopora_meandrina_HIv1___xfSc0000002 779520 9821613 12.5996 16.7128
Pocillopora_meandrina_HIv1___xfSc0000003 462347 3051398 6.5998 16.4105
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1543150 4.6095 8.063
Pocillopora_meandrina_HIv1___xfSc0000006 290100 985653 3.3976 7.2061
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2965296 11.755 14.7575
Pocillopora_meandrina_HIv1___xfSc0000012 148278 537445 3.6246 8.0008
Pocillopora_meandrina_HIv1___xfSc0000014 118081 29572 0.2504 1.0262
Pocillopora_meandrina_HIv1___xfSc0000017 98555 573066 5.8147 86.121
Pocillopora_meandrina_HIv1___xfSc0000021 95778 772791 8.0686 13.8383
Pocillopora_meandrina_HIv1___xfSc0000024 90744 636909 7.0187 9.7627
Pocillopora_meandrina_HIv1___xfSc0000029 85532 148843 1.7402 6.3884
Pocillopora_meandrina_HIv1___xfSc0000038 77395 48743 0.6298 6.7297
Pocillopora_meandrina_HIv1___xfSc0000058 69718 889514 12.7587 19.4403
Pocillopora_meandrina_HIv1___xfSc0000059 69426 896241 12.9093 16.2748
Pocillopora_meandrina_HIv1___xfSc0000074 66573 503450 7.5624 8.3962
Pocillopora_meandrina_HIv1___xfSc0000081 65415 280172 4.283 7.0332
Pocillopora_meandrina_HIv1___xfSc0000083 65317 821508 12.5772 10.7983
Pocillopora_meandrina_HIv1___xfSc0000092 63607 188403 2.962 7.2101
Pocillopora_meandrina_HIv1___xfSc0000094 62842 139592 2.2213 4.7745
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1034270 17.0796 18.3552
Pocillopora_meandrina_HIv1___xfSc0000132 59032 43907 0.7438 1.8131
Pocillopora_meandrina_HIv1___xfSc0000145 58221 210791 3.6205 5.9411
Pocillopora_meandrina_HIv1___xfSc0000146 58151 178885 3.0762 7.2072
Pocillopora_meandrina_HIv1___xfSc0000168 56681 409291 7.221 10.7309
Pocillopora_meandrina_HIv1___xfSc0000175 56271 371516 6.6023 16.6216
Pocillopora_meandrina_HIv1___xfSc0000195 55223 10447 0.1892 1.3205
Pocillopora_meandrina_HIv1___xfSc0000199 55095 534077 9.6937 13.3069
Pocillopora_meandrina_HIv1___xfSc0000205 54658 567647 10.3854 13.9229
Pocillopora_meandrina_HIv1___xfSc0000206 54623 292769 5.3598 7.981
Pocillopora_meandrina_HIv1___xfSc0000212 54299 436560 8.0399 11.6634
Pocillopora_meandrina_HIv1___xfSc0000217 54168 627858 11.5909 19.2627
Pocillopora_meandrina_HIv1___xfSc0000223 53823 416134 7.7315 9.1407
Pocillopora_meandrina_HIv1___xfSc0000228 53382 566379 10.6099 30.0699
Pocillopora_meandrina_HIv1___xfSc0000237 53049 369022 6.9562 8.9339
Pocillopora_meandrina_HIv1___xfSc0000262 52308 443601 8.4806 8.4794
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1096821 20.9862 31.269
Pocillopora_meandrina_HIv1___xfSc0000272 52107 503187 9.6568 12.5158
Pocillopora_meandrina_HIv1___xfSc0000275 51938 404252 7.7834 9.8975
Pocillopora_meandrina_HIv1___xfSc0000284 51483 627104 12.1808 15.895
Pocillopora_meandrina_HIv1___xfSc0000288 51367 448393 8.7292 21.3519
Pocillopora_meandrina_HIv1___xfSc0000300 50845 8560 0.1684 0.5195
Pocillopora_meandrina_HIv1___xfSc0000301 50809 500071 9.8422 11.9053
Pocillopora_meandrina_HIv1___xfSc0000343 49544 269115 5.4318 7.0818
Pocillopora_meandrina_HIv1___xfSc0000376 48519 333456 6.8727 19.1922
Pocillopora_meandrina_HIv1___xfSc0000415 47398 979792 20.6716 28.1442
Pocillopora_meandrina_HIv1___xfSc0000423 47202 66540 1.4097 3.9724
Pocillopora_meandrina_HIv1___xfSc0000426 47096 815327 17.312 20.5685
Pocillopora_meandrina_HIv1___xfSc0000428 47057 1044602 22.1987 30.9236
Pocillopora_meandrina_HIv1___xfSc0000436 46816 444817 9.5014 20.9373
Pocillopora_meandrina_HIv1___xfSc0000445 46561 89034 1.9122 4.4902
Pocillopora_meandrina_HIv1___xfSc0000447 46542 659451 14.1689 16.4911
Pocillopora_meandrina_HIv1___xfSc0000469 45938 636050 13.8458 11.7137
Pocillopora_meandrina_HIv1___xfSc0000477 45781 226730 4.9525 8.2098
Pocillopora_meandrina_HIv1___xfSc0000479 45736 241765 5.2861 8.2109
Pocillopora_meandrina_HIv1___xfSc0000482 45585 804557 17.6496 28.9186
Pocillopora_meandrina_HIv1___xfSc0000488 45379 97292 2.144 4.472
Pocillopora_meandrina_HIv1___xfSc0000506 44781 214474 4.7894 6.6012
Pocillopora_meandrina_HIv1___xfSc0000527 44235 303798 6.8678 9.6365
Pocillopora_meandrina_HIv1___xfSc0000540 43935 400954 9.1261 10.8061
Pocillopora_meandrina_HIv1___xfSc0000555 43535 134432 3.0879 8.2086
Pocillopora_meandrina_HIv1___xfSc0000565 43357 679955 15.6827 13.5537
Pocillopora_meandrina_HIv1___xfSc0000566 43316 272176 6.2835 9.5856
Pocillopora_meandrina_HIv1___xfSc0000567 43305 241815 5.584 11.0284
Pocillopora_meandrina_HIv1___xfSc0000570 43295 74702 1.7254 5.1661
Pocillopora_meandrina_HIv1___xfSc0000579 43029 75701 1.7593 4.2609
Pocillopora_meandrina_HIv1___xfSc0000583 42958 399871 9.3084 10.5176
Pocillopora_meandrina_HIv1___xfSc0000596 42675 343965 8.0601 12.6943
Pocillopora_meandrina_HIv1___xfSc0000612 42423 187612 4.4224 6.8477
Pocillopora_meandrina_HIv1___xfSc0000616 42355 3419879 80.7432 197.2013
Pocillopora_meandrina_HIv1___xfSc0000621 42164 359753 8.5322 10.7353
Pocillopora_meandrina_HIv1___xfSc0000642 41754 184988 4.4304 7.9279
Pocillopora_meandrina_HIv1___xfSc0000655 41446 163527 3.9455 6.8226
Pocillopora_meandrina_HIv1___xfSc0000692 40426 239355 5.9208 7.0284
Pocillopora_meandrina_HIv1___xfSc0000699 40296 44089 1.0941 2.4368
Pocillopora_meandrina_HIv1___xfSc0000704 40233 671218 16.6833 19.2517
Pocillopora_meandrina_HIv1___xfSc0000705 40197 158962 3.9546 7.4654
Pocillopora_meandrina_HIv1___xfSc0000716 39998 491616 12.291 12.6167
Pocillopora_meandrina_HIv1___xfSc0000725 39827 115940 2.9111 8.4108
Pocillopora_meandrina_HIv1___xfSc0000729 39775 20329 0.5111 3.2941
Pocillopora_meandrina_HIv1___xfSc0000760 39228 11524 0.2938 1.5391
Pocillopora_meandrina_HIv1___xfSc0000763 39151 295710 7.5531 7.7546
Pocillopora_meandrina_HIv1___xfSc0000765 39117 127078 3.2487 6.784
Pocillopora_meandrina_HIv1___xfSc0000788 38513 326053 8.4661 10.9506
Pocillopora_meandrina_HIv1___xfSc0000811 37888 217369 5.7371 8.2938
Pocillopora_meandrina_HIv1___xfSc0000812 37881 34030 0.8983 1.7529
Pocillopora_meandrina_HIv1___xfSc0000817 37779 668866 17.7047 11.8582
Pocillopora_meandrina_HIv1___xfSc0000824 37656 140325 3.7265 5.9128
Pocillopora_meandrina_HIv1___xfSc0000835 37434 280100 7.4825 9.1628
Pocillopora_meandrina_HIv1___xfSc0000836 37372 290631 7.7767 12.6212
Pocillopora_meandrina_HIv1___xfSc0000837 37368 619238 16.5713 13.3999
Pocillopora_meandrina_HIv1___xfSc0000840 37283 141268 3.7891 9.8442
Pocillopora_meandrina_HIv1___xfSc0000857 37006 125100 3.3805 5.5178
Pocillopora_meandrina_HIv1___xfSc0000859 36995 56643 1.5311 2.7238
Pocillopora_meandrina_HIv1___xfSc0000866 36925 78402 2.1233 3.8967
Pocillopora_meandrina_HIv1___xfSc0000868 36831 105114 2.854 8.721
Pocillopora_meandrina_HIv1___xfSc0000875 36611 37197 1.016 2.5499
Pocillopora_meandrina_HIv1___xfSc0000885 36416 186616 5.1246 6.2129
Pocillopora_meandrina_HIv1___xfSc0000886 36355 130304 3.5842 7.4835
Pocillopora_meandrina_HIv1___xfSc0000890 36339 259254 7.1343 9.463
Pocillopora_meandrina_HIv1___xfSc0000892 36267 45946 1.2669 3.4824
Pocillopora_meandrina_HIv1___xfSc0000943 35168 13055 0.3712 1.6404
Pocillopora_meandrina_HIv1___xfSc0000948 35100 327393 9.3274 12.5778
Pocillopora_meandrina_HIv1___xfSc0000952 34934 588304 16.8404 12.293
Pocillopora_meandrina_HIv1___xfSc0000953 34905 236968 6.7889 8.2286
Pocillopora_meandrina_HIv1___xfSc0000957 34773 506914 14.5778 18.346
Pocillopora_meandrina_HIv1___xfSc0000968 34345 16961 0.4938 1.7558
Pocillopora_meandrina_HIv1___xfSc0000974 34140 299038 8.7592 9.1639
Pocillopora_meandrina_HIv1___xfSc0000975 33988 379670 11.1707 10.8379
Pocillopora_meandrina_HIv1___xfSc0000995 33324 152174 4.5665 11.7421
Pocillopora_meandrina_HIv1___xfSc0001011 32918 330247 10.0324 23.9019
Pocillopora_meandrina_HIv1___xfSc0001122 29140 342968 11.7697 10.0529
Pocillopora_meandrina_HIv1___xfSc0001170 27381 36111 1.3188 3.1059
Pocillopora_meandrina_HIv1___xfSc0001179 27200 109081 4.0103 7.1358
Pocillopora_meandrina_HIv1___xfSc0001231 22938 24384 1.063 1.7172
Pocillopora_meandrina_HIv1___xfSc0001237 22715 51215 2.2547 6.8241
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1809309 4.4316 7.9904
Pocillopora_meandrina_HIv1___xpSc0001275 48561 240183 4.946 9.9045
Pocillopora_meandrina_HIv1___xpSc0001276 38618 41330 1.0702 3.685
Pocillopora_meandrina_HIv1___xpSc0001280 35955 358458 9.9696 14.0078
Pocillopora_meandrina_HIv1___xpSc0001281 34238 257689 7.5264 9.7594
Pocillopora_meandrina_HIv1___xpSc0001290 28931 299914 10.3665 12.4996
Pocillopora_meandrina_HIv1___xpSc0001321 15304 22883 1.4952 2.7976
Pocillopora_meandrina_HIv1___xpSc0001331 8958 170226 19.0027 12.5382
Pocillopora_meandrina_HIv1___xpSc0001337 6786 101083 14.8958 7.5998
Pocillopora_meandrina_HIv1___xpSc0001344 5647 106255 18.8162 22.5155
Pocillopora_meandrina_HIv1___xpSc0001355 3576 47165 13.1893 10.2828

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 22:43:57
    Generated by QualiMap v.2.3