Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-255-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-255-TP3_R1_001.fastp-trim.fq.gz -2 POC-255-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-255-TP3 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:12:34 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-255-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 46,391,150
Mapped reads 46,391,150 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 46,391,150 / 100%
Mapped reads, first in pair 23,195,575 / 50%
Mapped reads, second in pair 23,195,575 / 50%
Mapped reads, both in pair 46,391,150 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 115.73
Overlapping read pairs 19,756,799 / 85.17%
Duplicated reads (estimated) 6,735,265 / 14.52%
Duplication rate 13.32%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,116,190,900 / 39.58%
Number/percentage of C's 556,765,573 / 10.41%
Number/percentage of T's 2,124,455,665 / 39.73%
Number/percentage of G's 549,672,988 / 10.28%
Number/percentage of N's 103,090 / 0%
GC Percentage 20.69%

Coverage

Mean 14.2397
Standard Deviation 22.516
Mean (paired-end reads overlap ignored) 9.99

Mapping Quality

Mean Mapping Quality 22.77

Insert size

Mean 172.54
Standard Deviation 85.67
P25/Median/P75 111 / 144 / 216

Mismatches and indels

General error rate 21.77%
Mismatches 1,145,691,871
Insertions 7,525,282
Mapped reads with at least one insertion 12.17%
Deletions 5,773,618
Mapped reads with at least one deletion 10.54%
Homopolymer indels 50.21%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 336445690 15.5394 14.4528
Pocillopora_meandrina_HIv1___Sc0000001 21507942 347425694 16.1534 14.578
Pocillopora_meandrina_HIv1___Sc0000002 19741974 310018326 15.7035 13.4056
Pocillopora_meandrina_HIv1___Sc0000003 19417450 272029215 14.0095 14.3713
Pocillopora_meandrina_HIv1___Sc0000004 14584444 202785320 13.9042 23.9656
Pocillopora_meandrina_HIv1___Sc0000005 14098929 211664375 15.0128 13.2004
Pocillopora_meandrina_HIv1___Sc0000006 14068054 212346424 15.0942 14.3876
Pocillopora_meandrina_HIv1___Sc0000007 13590779 204451150 15.0434 14.9838
Pocillopora_meandrina_HIv1___Sc0000008 12446599 198057336 15.9126 14.9485
Pocillopora_meandrina_HIv1___Sc0000009 11983232 102100785 8.5203 20.2986
Pocillopora_meandrina_HIv1___Sc0000010 11763137 168970395 14.3644 18.0287
Pocillopora_meandrina_HIv1___Sc0000011 10501528 183016852 17.4276 12.6505
Pocillopora_meandrina_HIv1___Sc0000012 10024633 152087565 15.1714 37.9813
Pocillopora_meandrina_HIv1___Sc0000013 9946974 106670097 10.7239 12.824
Pocillopora_meandrina_HIv1___Sc0000014 9536826 150874885 15.8202 13.2198
Pocillopora_meandrina_HIv1___Sc0000015 9393205 136051494 14.484 13.775
Pocillopora_meandrina_HIv1___Sc0000016 9288165 133284768 14.35 13.7498
Pocillopora_meandrina_HIv1___Sc0000017 9274345 137781268 14.8562 14.3395
Pocillopora_meandrina_HIv1___Sc0000018 8584156 133194292 15.5163 13.214
Pocillopora_meandrina_HIv1___Sc0000019 7112774 107983214 15.1816 15.677
Pocillopora_meandrina_HIv1___Sc0000020 6748058 101740446 15.077 14.8768
Pocillopora_meandrina_HIv1___Sc0000021 6546105 101934134 15.5717 12.9095
Pocillopora_meandrina_HIv1___Sc0000022 6319256 87431820 13.8358 19.2681
Pocillopora_meandrina_HIv1___Sc0000023 5767069 72406469 12.5552 13.8617
Pocillopora_meandrina_HIv1___Sc0000024 5762297 58352871 10.1267 13.6905
Pocillopora_meandrina_HIv1___Sc0000025 5759531 70993097 12.3262 14.4147
Pocillopora_meandrina_HIv1___Sc0000026 5647578 99144575 17.5552 25.2734
Pocillopora_meandrina_HIv1___Sc0000027 5550630 67044156 12.0787 18.4409
Pocillopora_meandrina_HIv1___Sc0000028 5130920 83427227 16.2597 15.9626
Pocillopora_meandrina_HIv1___Sc0000029 4860867 65290444 13.4319 15.8715
Pocillopora_meandrina_HIv1___Sc0000030 4843735 76231185 15.7381 16.2636
Pocillopora_meandrina_HIv1___Sc0000031 4691590 71913484 15.3282 15.6224
Pocillopora_meandrina_HIv1___Sc0000032 3615800 58421970 16.1574 16.756
Pocillopora_meandrina_HIv1___Sc0000033 3306609 38631463 11.6831 17.7166
Pocillopora_meandrina_HIv1___Sc0000034 3122802 49115334 15.728 13.3445
Pocillopora_meandrina_HIv1___Sc0000035 3015365 35235222 11.6852 16.7585
Pocillopora_meandrina_HIv1___Sc0000036 3007169 48962716 16.282 12.521
Pocillopora_meandrina_HIv1___Sc0000037 2860435 42040483 14.6972 24.685
Pocillopora_meandrina_HIv1___Sc0000038 2701138 38438887 14.2306 20.1007
Pocillopora_meandrina_HIv1___Sc0000039 2599273 31260460 12.0266 52.701
Pocillopora_meandrina_HIv1___Sc0000040 2445666 38504551 15.744 18.112
Pocillopora_meandrina_HIv1___Sc0000041 2159376 36813312 17.0481 15.4045
Pocillopora_meandrina_HIv1___Sc0000042 1957488 24242010 12.3842 13.3663
Pocillopora_meandrina_HIv1___Sc0000043 1845599 22984946 12.4539 13.0242
Pocillopora_meandrina_HIv1___Sc0000044 1724711 26109536 15.1385 14.9016
Pocillopora_meandrina_HIv1___Sc0000045 1153740 14887942 12.9041 13.1398
Pocillopora_meandrina_HIv1___Sc0000046 755410 7567934 10.0183 16.4396
Pocillopora_meandrina_HIv1___Sc0000047 239089 1603290 6.7058 9.6179
Pocillopora_meandrina_HIv1___Sc0000048 214660 55724 0.2596 1.8175
Pocillopora_meandrina_HIv1___Sc0000049 179266 599036 3.3416 7.041
Pocillopora_meandrina_HIv1___Sc0000050 177168 195720 1.1047 4.7073
Pocillopora_meandrina_HIv1___Sc0000051 165057 658719 3.9909 6.7569
Pocillopora_meandrina_HIv1___Sc0000052 155210 91633 0.5904 6.9572
Pocillopora_meandrina_HIv1___Sc0000053 123249 328940 2.6689 6.8144
Pocillopora_meandrina_HIv1___Sc0000054 122643 1873963 15.2798 25.8523
Pocillopora_meandrina_HIv1___Sc0000055 121609 761889 6.2651 20.1036
Pocillopora_meandrina_HIv1___Sc0000056 112816 43755 0.3878 3.5874
Pocillopora_meandrina_HIv1___Sc0000057 107171 240014 2.2395 6.0702
Pocillopora_meandrina_HIv1___Sc0000058 98341 49085 0.4991 4.3357
Pocillopora_meandrina_HIv1___Sc0000059 83292 11439 0.1373 0.661
Pocillopora_meandrina_HIv1___Sc0000060 79483 95 0.0012 0.0447
Pocillopora_meandrina_HIv1___Sc0000061 75390 299509 3.9728 10.2865
Pocillopora_meandrina_HIv1___Sc0000062 74194 15581 0.21 1.1646
Pocillopora_meandrina_HIv1___Sc0000063 73457 14786 0.2013 2.3015
Pocillopora_meandrina_HIv1___Sc0000064 72700 4704 0.0647 0.4379
Pocillopora_meandrina_HIv1___Sc0000065 67986 4431 0.0652 0.716
Pocillopora_meandrina_HIv1___Sc0000066 66659 364362 5.4661 6.8628
Pocillopora_meandrina_HIv1___Sc0000067 64947 136397 2.1001 4.351
Pocillopora_meandrina_HIv1___Sc0000068 64340 40583 0.6308 2.0901
Pocillopora_meandrina_HIv1___Sc0000069 62616 300894 4.8054 7.6765
Pocillopora_meandrina_HIv1___Sc0000070 60121 283077 4.7085 31.1728
Pocillopora_meandrina_HIv1___Sc0000071 57157 61652 1.0786 2.957
Pocillopora_meandrina_HIv1___Sc0000072 56626 12616 0.2228 1.9973
Pocillopora_meandrina_HIv1___Sc0000073 56082 10298 0.1836 0.6095
Pocillopora_meandrina_HIv1___Sc0000074 55210 714 0.0129 0.1452
Pocillopora_meandrina_HIv1___Sc0000075 54685 2011 0.0368 0.3902
Pocillopora_meandrina_HIv1___Sc0000076 54587 192557 3.5275 18.5376
Pocillopora_meandrina_HIv1___Sc0000077 53379 14742 0.2762 0.8031
Pocillopora_meandrina_HIv1___Sc0000078 51564 377 0.0073 0.1179
Pocillopora_meandrina_HIv1___Sc0000079 49664 2493 0.0502 0.317
Pocillopora_meandrina_HIv1___Sc0000080 47218 115220 2.4402 7.1247
Pocillopora_meandrina_HIv1___Sc0000081 42490 10867 0.2558 0.8955
Pocillopora_meandrina_HIv1___Sc0000082 32657 716826 21.9501 45.0961
Pocillopora_meandrina_HIv1___Sc0000083 27992 77237 2.7593 2.2785
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 10094841 6.3029 11.8726
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5881454 4.9105 9.0539
Pocillopora_meandrina_HIv1___xfSc0000002 779520 6423212 8.24 12.5182
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1422839 3.0774 5.7235
Pocillopora_meandrina_HIv1___xfSc0000004 334777 874946 2.6135 5.2911
Pocillopora_meandrina_HIv1___xfSc0000006 290100 487076 1.679 4.0682
Pocillopora_meandrina_HIv1___xfSc0000007 252258 585570 2.3213 4.8875
Pocillopora_meandrina_HIv1___xfSc0000012 148278 904876 6.1026 12.449
Pocillopora_meandrina_HIv1___xfSc0000014 118081 16989 0.1439 0.6258
Pocillopora_meandrina_HIv1___xfSc0000017 98555 357330 3.6257 59.1054
Pocillopora_meandrina_HIv1___xfSc0000021 95778 367298 3.8349 8.1955
Pocillopora_meandrina_HIv1___xfSc0000024 90744 969869 10.688 15.8118
Pocillopora_meandrina_HIv1___xfSc0000029 85532 343854 4.0202 14.5459
Pocillopora_meandrina_HIv1___xfSc0000038 77395 19547 0.2526 1.8687
Pocillopora_meandrina_HIv1___xfSc0000058 69718 771910 11.0719 13.1963
Pocillopora_meandrina_HIv1___xfSc0000059 69426 516635 7.4415 10.5333
Pocillopora_meandrina_HIv1___xfSc0000074 66573 366170 5.5003 8.0221
Pocillopora_meandrina_HIv1___xfSc0000081 65415 354126 5.4135 7.961
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1160685 17.77 45.8421
Pocillopora_meandrina_HIv1___xfSc0000092 63607 647735 10.1834 9.99
Pocillopora_meandrina_HIv1___xfSc0000094 62842 184446 2.9351 6.3898
Pocillopora_meandrina_HIv1___xfSc0000113 60556 811116 13.3945 14.6697
Pocillopora_meandrina_HIv1___xfSc0000132 59032 353303 5.9849 9.4771
Pocillopora_meandrina_HIv1___xfSc0000145 58221 458788 7.8801 9.0903
Pocillopora_meandrina_HIv1___xfSc0000146 58151 457977 7.8757 10.2066
Pocillopora_meandrina_HIv1___xfSc0000168 56681 338691 5.9754 8.72
Pocillopora_meandrina_HIv1___xfSc0000175 56271 151652 2.695 6.7762
Pocillopora_meandrina_HIv1___xfSc0000195 55223 86592 1.568 5.3671
Pocillopora_meandrina_HIv1___xfSc0000199 55095 225356 4.0903 9.4497
Pocillopora_meandrina_HIv1___xfSc0000205 54658 415754 7.6065 11.5927
Pocillopora_meandrina_HIv1___xfSc0000206 54623 190798 3.493 5.8037
Pocillopora_meandrina_HIv1___xfSc0000212 54299 349548 6.4375 19.4442
Pocillopora_meandrina_HIv1___xfSc0000217 54168 311755 5.7553 13.151
Pocillopora_meandrina_HIv1___xfSc0000223 53823 235952 4.3839 6.6682
Pocillopora_meandrina_HIv1___xfSc0000228 53382 458876 8.5961 28.7863
Pocillopora_meandrina_HIv1___xfSc0000237 53049 304440 5.7388 7.5645
Pocillopora_meandrina_HIv1___xfSc0000262 52308 217145 4.1513 6.9622
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2363546 45.2232 54.6405
Pocillopora_meandrina_HIv1___xfSc0000272 52107 400203 7.6804 10.4347
Pocillopora_meandrina_HIv1___xfSc0000275 51938 348027 6.7008 9.9807
Pocillopora_meandrina_HIv1___xfSc0000284 51483 517195 10.0459 14.8437
Pocillopora_meandrina_HIv1___xfSc0000288 51367 698058 13.5896 12.9528
Pocillopora_meandrina_HIv1___xfSc0000300 50845 7548 0.1485 0.7024
Pocillopora_meandrina_HIv1___xfSc0000301 50809 380516 7.4891 10.0651
Pocillopora_meandrina_HIv1___xfSc0000343 49544 150299 3.0336 5.2298
Pocillopora_meandrina_HIv1___xfSc0000376 48519 400192 8.2482 22.1642
Pocillopora_meandrina_HIv1___xfSc0000415 47398 234665 4.9509 9.3798
Pocillopora_meandrina_HIv1___xfSc0000423 47202 57712 1.2227 2.7843
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1969731 41.8237 36.5619
Pocillopora_meandrina_HIv1___xfSc0000428 47057 320420 6.8092 13.4506
Pocillopora_meandrina_HIv1___xfSc0000436 46816 406501 8.683 14.0913
Pocillopora_meandrina_HIv1___xfSc0000445 46561 165582 3.5562 5.1952
Pocillopora_meandrina_HIv1___xfSc0000447 46542 244879 5.2615 6.9437
Pocillopora_meandrina_HIv1___xfSc0000469 45938 381544 8.3056 7.6946
Pocillopora_meandrina_HIv1___xfSc0000477 45781 131736 2.8775 4.7787
Pocillopora_meandrina_HIv1___xfSc0000479 45736 151387 3.31 5.8128
Pocillopora_meandrina_HIv1___xfSc0000482 45585 786628 17.2563 24.8759
Pocillopora_meandrina_HIv1___xfSc0000488 45379 186437 4.1084 7.1333
Pocillopora_meandrina_HIv1___xfSc0000506 44781 169080 3.7757 5.8667
Pocillopora_meandrina_HIv1___xfSc0000527 44235 217839 4.9246 7.2196
Pocillopora_meandrina_HIv1___xfSc0000540 43935 284218 6.4691 9.0549
Pocillopora_meandrina_HIv1___xfSc0000555 43535 198730 4.5648 9.4567
Pocillopora_meandrina_HIv1___xfSc0000565 43357 569839 13.143 15.191
Pocillopora_meandrina_HIv1___xfSc0000566 43316 241237 5.5692 7.233
Pocillopora_meandrina_HIv1___xfSc0000567 43305 163616 3.7782 7.8057
Pocillopora_meandrina_HIv1___xfSc0000570 43295 122059 2.8192 4.4707
Pocillopora_meandrina_HIv1___xfSc0000579 43029 77210 1.7944 4.1987
Pocillopora_meandrina_HIv1___xfSc0000583 42958 280799 6.5366 8.0544
Pocillopora_meandrina_HIv1___xfSc0000596 42675 296423 6.9461 10.702
Pocillopora_meandrina_HIv1___xfSc0000612 42423 180696 4.2594 5.6794
Pocillopora_meandrina_HIv1___xfSc0000616 42355 12852914 303.4568 1,319.2429
Pocillopora_meandrina_HIv1___xfSc0000621 42164 471355 11.1791 15.3087
Pocillopora_meandrina_HIv1___xfSc0000642 41754 320327 7.6718 11.3055
Pocillopora_meandrina_HIv1___xfSc0000655 41446 134498 3.2451 7.6245
Pocillopora_meandrina_HIv1___xfSc0000692 40426 154176 3.8138 6.4342
Pocillopora_meandrina_HIv1___xfSc0000699 40296 21129 0.5243 1.7178
Pocillopora_meandrina_HIv1___xfSc0000704 40233 430597 10.7026 15.6383
Pocillopora_meandrina_HIv1___xfSc0000705 40197 133957 3.3325 5.2728
Pocillopora_meandrina_HIv1___xfSc0000716 39998 197501 4.9378 7.9519
Pocillopora_meandrina_HIv1___xfSc0000725 39827 167706 4.2109 10.1545
Pocillopora_meandrina_HIv1___xfSc0000729 39775 9675 0.2432 0.9633
Pocillopora_meandrina_HIv1___xfSc0000760 39228 3697 0.0942 0.4126
Pocillopora_meandrina_HIv1___xfSc0000763 39151 258990 6.6152 6.3315
Pocillopora_meandrina_HIv1___xfSc0000765 39117 116168 2.9698 5.5218
Pocillopora_meandrina_HIv1___xfSc0000788 38513 536679 13.935 15.2605
Pocillopora_meandrina_HIv1___xfSc0000811 37888 447509 11.8114 11.0514
Pocillopora_meandrina_HIv1___xfSc0000812 37881 13167 0.3476 0.9132
Pocillopora_meandrina_HIv1___xfSc0000817 37779 432622 11.4514 9.675
Pocillopora_meandrina_HIv1___xfSc0000824 37656 70978 1.8849 3.7361
Pocillopora_meandrina_HIv1___xfSc0000835 37434 227963 6.0897 8.3149
Pocillopora_meandrina_HIv1___xfSc0000836 37372 203043 5.433 8.7142
Pocillopora_meandrina_HIv1___xfSc0000837 37368 397765 10.6445 8.4565
Pocillopora_meandrina_HIv1___xfSc0000840 37283 241456 6.4763 9.7625
Pocillopora_meandrina_HIv1___xfSc0000857 37006 99430 2.6869 5.3939
Pocillopora_meandrina_HIv1___xfSc0000859 36995 48670 1.3156 3.4563
Pocillopora_meandrina_HIv1___xfSc0000866 36925 87522 2.3703 5.2007
Pocillopora_meandrina_HIv1___xfSc0000868 36831 120570 3.2736 9.2009
Pocillopora_meandrina_HIv1___xfSc0000875 36611 125498 3.4279 9.5008
Pocillopora_meandrina_HIv1___xfSc0000885 36416 129062 3.5441 5.5698
Pocillopora_meandrina_HIv1___xfSc0000886 36355 188048 5.1725 8.7658
Pocillopora_meandrina_HIv1___xfSc0000890 36339 242319 6.6683 11.2775
Pocillopora_meandrina_HIv1___xfSc0000892 36267 194096 5.3519 33.5014
Pocillopora_meandrina_HIv1___xfSc0000943 35168 4955 0.1409 0.6025
Pocillopora_meandrina_HIv1___xfSc0000948 35100 277884 7.9169 9.8182
Pocillopora_meandrina_HIv1___xfSc0000952 34934 146388 4.1904 6.2558
Pocillopora_meandrina_HIv1___xfSc0000953 34905 129777 3.718 5.6743
Pocillopora_meandrina_HIv1___xfSc0000957 34773 128557 3.697 7.8167
Pocillopora_meandrina_HIv1___xfSc0000968 34345 38171 1.1114 3.476
Pocillopora_meandrina_HIv1___xfSc0000974 34140 363757 10.6549 12.0828
Pocillopora_meandrina_HIv1___xfSc0000975 33988 323943 9.5311 11.4589
Pocillopora_meandrina_HIv1___xfSc0000995 33324 64043 1.9218 4.4745
Pocillopora_meandrina_HIv1___xfSc0001011 32918 289488 8.7942 10.0257
Pocillopora_meandrina_HIv1___xfSc0001122 29140 200941 6.8957 9.2896
Pocillopora_meandrina_HIv1___xfSc0001170 27381 57947 2.1163 8.3792
Pocillopora_meandrina_HIv1___xfSc0001179 27200 72614 2.6696 4.9623
Pocillopora_meandrina_HIv1___xfSc0001231 22938 13090 0.5707 1.2618
Pocillopora_meandrina_HIv1___xfSc0001237 22715 124279 5.4712 14.6617
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2794211 6.844 12.5658
Pocillopora_meandrina_HIv1___xpSc0001275 48561 220883 4.5486 9.8116
Pocillopora_meandrina_HIv1___xpSc0001276 38618 98938 2.562 6.0114
Pocillopora_meandrina_HIv1___xpSc0001280 35955 173862 4.8355 7.9755
Pocillopora_meandrina_HIv1___xpSc0001281 34238 431168 12.5933 43.5726
Pocillopora_meandrina_HIv1___xpSc0001290 28931 244766 8.4603 7.4942
Pocillopora_meandrina_HIv1___xpSc0001321 15304 92087 6.0172 10.6844
Pocillopora_meandrina_HIv1___xpSc0001331 8958 149815 16.7242 11.0286
Pocillopora_meandrina_HIv1___xpSc0001337 6786 11165 1.6453 3.4709
Pocillopora_meandrina_HIv1___xpSc0001344 5647 37523 6.6448 10.7705
Pocillopora_meandrina_HIv1___xpSc0001355 3576 37110 10.3775 8.6945

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 21:12:38
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