Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-52-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-52-TP4_R1_001.fastp-trim.fq.gz -2 POC-52-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-52-TP4 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:58:45 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-52-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 38,106,216
Mapped reads 38,106,216 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 38,106,216 / 100%
Mapped reads, first in pair 19,053,108 / 50%
Mapped reads, second in pair 19,053,108 / 50%
Mapped reads, both in pair 38,106,216 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.57
Overlapping read pairs 11,661,961 / 61.21%
Duplicated reads (estimated) 3,912,624 / 10.27%
Duplication rate 9.85%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,011,984,300 / 40.31%
Number/percentage of C's 487,903,854 / 9.78%
Number/percentage of T's 2,012,870,428 / 40.33%
Number/percentage of G's 477,774,636 / 9.57%
Number/percentage of N's 448,584 / 0.01%
GC Percentage 19.35%

Coverage

Mean 13.2968
Standard Deviation 11.7968
Mean (paired-end reads overlap ignored) 11.19

Mapping Quality

Mean Mapping Quality 22.4

Insert size

Mean 248.87
Standard Deviation 88.8
P25/Median/P75 180 / 242 / 307

Mismatches and indels

General error rate 21.2%
Mismatches 1,038,681,502
Insertions 7,697,662
Mapped reads with at least one insertion 15.11%
Deletions 6,126,489
Mapped reads with at least one deletion 13.43%
Homopolymer indels 52.1%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 302539213 13.9734 10.168
Pocillopora_meandrina_HIv1___Sc0000001 21507942 321887586 14.966 10.1761
Pocillopora_meandrina_HIv1___Sc0000002 19741974 288342044 14.6055 10.011
Pocillopora_meandrina_HIv1___Sc0000003 19417450 255779538 13.1727 11.7405
Pocillopora_meandrina_HIv1___Sc0000004 14584444 191454931 13.1273 19.4936
Pocillopora_meandrina_HIv1___Sc0000005 14098929 197968868 14.0414 9.4691
Pocillopora_meandrina_HIv1___Sc0000006 14068054 196843737 13.9923 11.5097
Pocillopora_meandrina_HIv1___Sc0000007 13590779 189227144 13.9232 10.9707
Pocillopora_meandrina_HIv1___Sc0000008 12446599 185163444 14.8766 10.6397
Pocillopora_meandrina_HIv1___Sc0000009 11983232 124882561 10.4214 16.4185
Pocillopora_meandrina_HIv1___Sc0000010 11763137 156808336 13.3305 12.3363
Pocillopora_meandrina_HIv1___Sc0000011 10501528 169094983 16.1019 9.7521
Pocillopora_meandrina_HIv1___Sc0000012 10024633 141338713 14.0991 11.7917
Pocillopora_meandrina_HIv1___Sc0000013 9946974 108259378 10.8836 10.5276
Pocillopora_meandrina_HIv1___Sc0000014 9536826 143945324 15.0936 10.0339
Pocillopora_meandrina_HIv1___Sc0000015 9393205 126087751 13.4233 9.9779
Pocillopora_meandrina_HIv1___Sc0000016 9288165 121602929 13.0922 10.0627
Pocillopora_meandrina_HIv1___Sc0000017 9274345 124203065 13.3921 9.9984
Pocillopora_meandrina_HIv1___Sc0000018 8584156 121381234 14.1401 9.7727
Pocillopora_meandrina_HIv1___Sc0000019 7112774 98089010 13.7905 11.0881
Pocillopora_meandrina_HIv1___Sc0000020 6748058 98254522 14.5604 13.3536
Pocillopora_meandrina_HIv1___Sc0000021 6546105 95480892 14.5859 9.9039
Pocillopora_meandrina_HIv1___Sc0000022 6319256 80150420 12.6835 12.6146
Pocillopora_meandrina_HIv1___Sc0000023 5767069 66748239 11.574 10.5697
Pocillopora_meandrina_HIv1___Sc0000024 5762297 54635565 9.4816 11.0577
Pocillopora_meandrina_HIv1___Sc0000025 5759531 71401421 12.3971 11.8826
Pocillopora_meandrina_HIv1___Sc0000026 5647578 89329905 15.8174 9.4306
Pocillopora_meandrina_HIv1___Sc0000027 5550630 70184193 12.6444 14.7236
Pocillopora_meandrina_HIv1___Sc0000028 5130920 76625965 14.9342 11.4167
Pocillopora_meandrina_HIv1___Sc0000029 4860867 54550658 11.2224 10.4315
Pocillopora_meandrina_HIv1___Sc0000030 4843735 71603807 14.7828 9.9928
Pocillopora_meandrina_HIv1___Sc0000031 4691590 64884000 13.8299 10.0351
Pocillopora_meandrina_HIv1___Sc0000032 3615800 54586897 15.0968 10.9348
Pocillopora_meandrina_HIv1___Sc0000033 3306609 36620260 11.0749 11.1434
Pocillopora_meandrina_HIv1___Sc0000034 3122802 45736988 14.6461 10.1544
Pocillopora_meandrina_HIv1___Sc0000035 3015365 32859394 10.8973 12.266
Pocillopora_meandrina_HIv1___Sc0000036 3007169 51163530 17.0139 9.8891
Pocillopora_meandrina_HIv1___Sc0000037 2860435 37957719 13.2699 11.2814
Pocillopora_meandrina_HIv1___Sc0000038 2701138 34088459 12.62 12.3064
Pocillopora_meandrina_HIv1___Sc0000039 2599273 28712608 11.0464 12.7928
Pocillopora_meandrina_HIv1___Sc0000040 2445666 29830062 12.1971 11.5316
Pocillopora_meandrina_HIv1___Sc0000041 2159376 31839932 14.745 10.3496
Pocillopora_meandrina_HIv1___Sc0000042 1957488 25137567 12.8417 10.4263
Pocillopora_meandrina_HIv1___Sc0000043 1845599 21406223 11.5985 9.5956
Pocillopora_meandrina_HIv1___Sc0000044 1724711 25222594 14.6242 10.5249
Pocillopora_meandrina_HIv1___Sc0000045 1153740 12840635 11.1296 10.1301
Pocillopora_meandrina_HIv1___Sc0000046 755410 7240540 9.5849 11.9889
Pocillopora_meandrina_HIv1___Sc0000047 239089 698113 2.9199 4.2346
Pocillopora_meandrina_HIv1___Sc0000048 214660 67167 0.3129 1.8108
Pocillopora_meandrina_HIv1___Sc0000049 179266 643522 3.5898 7.8189
Pocillopora_meandrina_HIv1___Sc0000050 177168 196382 1.1085 2.76
Pocillopora_meandrina_HIv1___Sc0000051 165057 874212 5.2964 8.1205
Pocillopora_meandrina_HIv1___Sc0000052 155210 24471 0.1577 1.5419
Pocillopora_meandrina_HIv1___Sc0000053 123249 227997 1.8499 5.5748
Pocillopora_meandrina_HIv1___Sc0000054 122643 1702965 13.8855 20.2579
Pocillopora_meandrina_HIv1___Sc0000055 121609 522328 4.2951 8.5891
Pocillopora_meandrina_HIv1___Sc0000056 112816 48260 0.4278 3.9537
Pocillopora_meandrina_HIv1___Sc0000057 107171 413298 3.8564 8.8992
Pocillopora_meandrina_HIv1___Sc0000058 98341 27074 0.2753 2.6486
Pocillopora_meandrina_HIv1___Sc0000059 83292 6685 0.0803 0.4344
Pocillopora_meandrina_HIv1___Sc0000060 79483 118 0.0015 0.0509
Pocillopora_meandrina_HIv1___Sc0000061 75390 314761 4.1751 9.2768
Pocillopora_meandrina_HIv1___Sc0000062 74194 15737 0.2121 1.0799
Pocillopora_meandrina_HIv1___Sc0000063 73457 37812 0.5148 4.864
Pocillopora_meandrina_HIv1___Sc0000064 72700 4814 0.0662 0.3593
Pocillopora_meandrina_HIv1___Sc0000065 67986 4506 0.0663 0.5324
Pocillopora_meandrina_HIv1___Sc0000066 66659 401132 6.0177 6.4893
Pocillopora_meandrina_HIv1___Sc0000067 64947 151442 2.3318 4.2242
Pocillopora_meandrina_HIv1___Sc0000068 64340 26528 0.4123 1.2508
Pocillopora_meandrina_HIv1___Sc0000069 62616 290399 4.6378 6.1458
Pocillopora_meandrina_HIv1___Sc0000070 60121 32994 0.5488 2.4275
Pocillopora_meandrina_HIv1___Sc0000071 57157 42384 0.7415 1.9077
Pocillopora_meandrina_HIv1___Sc0000072 56626 14609 0.258 2.7145
Pocillopora_meandrina_HIv1___Sc0000073 56082 14525 0.259 1.2097
Pocillopora_meandrina_HIv1___Sc0000074 55210 805 0.0146 0.1417
Pocillopora_meandrina_HIv1___Sc0000075 54685 1904 0.0348 0.2537
Pocillopora_meandrina_HIv1___Sc0000076 54587 148927 2.7283 13.705
Pocillopora_meandrina_HIv1___Sc0000077 53379 17153 0.3213 0.8117
Pocillopora_meandrina_HIv1___Sc0000078 51564 247 0.0048 0.0948
Pocillopora_meandrina_HIv1___Sc0000079 49664 1093 0.022 0.164
Pocillopora_meandrina_HIv1___Sc0000080 47218 85470 1.8101 4.3927
Pocillopora_meandrina_HIv1___Sc0000081 42490 9803 0.2307 0.7055
Pocillopora_meandrina_HIv1___Sc0000082 32657 734730 22.4984 43.3704
Pocillopora_meandrina_HIv1___Sc0000083 27992 83107 2.969 2.1306
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 11714951 7.3145 11.7146
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 6247383 5.2161 8.427
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5805826 7.448 9.0397
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2042405 4.4175 7.416
Pocillopora_meandrina_HIv1___xfSc0000004 334777 721968 2.1566 4.2958
Pocillopora_meandrina_HIv1___xfSc0000006 290100 624673 2.1533 3.9221
Pocillopora_meandrina_HIv1___xfSc0000007 252258 588974 2.3348 4.3753
Pocillopora_meandrina_HIv1___xfSc0000012 148278 863422 5.823 7.0316
Pocillopora_meandrina_HIv1___xfSc0000014 118081 17894 0.1515 0.6884
Pocillopora_meandrina_HIv1___xfSc0000017 98555 457236 4.6394 68.9374
Pocillopora_meandrina_HIv1___xfSc0000021 95778 559582 5.8425 10.382
Pocillopora_meandrina_HIv1___xfSc0000024 90744 502263 5.5349 8.0261
Pocillopora_meandrina_HIv1___xfSc0000029 85532 83209 0.9728 3.6263
Pocillopora_meandrina_HIv1___xfSc0000038 77395 64540 0.8339 8.4931
Pocillopora_meandrina_HIv1___xfSc0000058 69718 535978 7.6878 10.9387
Pocillopora_meandrina_HIv1___xfSc0000059 69426 392846 5.6585 10.0617
Pocillopora_meandrina_HIv1___xfSc0000074 66573 658366 9.8894 8.7824
Pocillopora_meandrina_HIv1___xfSc0000081 65415 555209 8.4875 7.4301
Pocillopora_meandrina_HIv1___xfSc0000083 65317 870762 13.3313 12.6011
Pocillopora_meandrina_HIv1___xfSc0000092 63607 507269 7.975 7.5349
Pocillopora_meandrina_HIv1___xfSc0000094 62842 103901 1.6534 3.7028
Pocillopora_meandrina_HIv1___xfSc0000113 60556 786394 12.9862 12.4569
Pocillopora_meandrina_HIv1___xfSc0000132 59032 449385 7.6126 9.7786
Pocillopora_meandrina_HIv1___xfSc0000145 58221 266616 4.5794 4.8966
Pocillopora_meandrina_HIv1___xfSc0000146 58151 347972 5.9839 7.0828
Pocillopora_meandrina_HIv1___xfSc0000168 56681 351527 6.2018 7.4238
Pocillopora_meandrina_HIv1___xfSc0000175 56271 215595 3.8314 9.8604
Pocillopora_meandrina_HIv1___xfSc0000195 55223 85646 1.5509 3.3322
Pocillopora_meandrina_HIv1___xfSc0000199 55095 360255 6.5388 13.2581
Pocillopora_meandrina_HIv1___xfSc0000205 54658 101344 1.8541 2.8999
Pocillopora_meandrina_HIv1___xfSc0000206 54623 218311 3.9967 6.1753
Pocillopora_meandrina_HIv1___xfSc0000212 54299 291685 5.3718 7.5474
Pocillopora_meandrina_HIv1___xfSc0000217 54168 317267 5.8571 10.1121
Pocillopora_meandrina_HIv1___xfSc0000223 53823 439901 8.1731 7.4029
Pocillopora_meandrina_HIv1___xfSc0000228 53382 440570 8.2532 23.846
Pocillopora_meandrina_HIv1___xfSc0000237 53049 291976 5.5039 6.6148
Pocillopora_meandrina_HIv1___xfSc0000262 52308 223311 4.2692 5.8275
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2454619 46.9658 37.3786
Pocillopora_meandrina_HIv1___xfSc0000272 52107 268367 5.1503 7.093
Pocillopora_meandrina_HIv1___xfSc0000275 51938 465219 8.9572 9.7005
Pocillopora_meandrina_HIv1___xfSc0000284 51483 480064 9.3247 10.7377
Pocillopora_meandrina_HIv1___xfSc0000288 51367 274931 5.3523 9.4462
Pocillopora_meandrina_HIv1___xfSc0000300 50845 16823 0.3309 1.2043
Pocillopora_meandrina_HIv1___xfSc0000301 50809 458122 9.0166 8.9697
Pocillopora_meandrina_HIv1___xfSc0000343 49544 170319 3.4377 6.5124
Pocillopora_meandrina_HIv1___xfSc0000376 48519 399936 8.2429 23.161
Pocillopora_meandrina_HIv1___xfSc0000415 47398 282986 5.9704 6.2736
Pocillopora_meandrina_HIv1___xfSc0000423 47202 78921 1.672 4.0377
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1223223 25.973 22.1901
Pocillopora_meandrina_HIv1___xfSc0000428 47057 503240 10.6943 15.7605
Pocillopora_meandrina_HIv1___xfSc0000436 46816 363685 7.7684 13.663
Pocillopora_meandrina_HIv1___xfSc0000445 46561 156453 3.3602 3.8624
Pocillopora_meandrina_HIv1___xfSc0000447 46542 438407 9.4196 11.3893
Pocillopora_meandrina_HIv1___xfSc0000469 45938 391478 8.5219 6.8271
Pocillopora_meandrina_HIv1___xfSc0000477 45781 253720 5.542 6.4191
Pocillopora_meandrina_HIv1___xfSc0000479 45736 154574 3.3797 4.9347
Pocillopora_meandrina_HIv1___xfSc0000482 45585 628704 13.7919 19.5133
Pocillopora_meandrina_HIv1___xfSc0000488 45379 184046 4.0558 5.5473
Pocillopora_meandrina_HIv1___xfSc0000506 44781 245979 5.4929 8.1491
Pocillopora_meandrina_HIv1___xfSc0000527 44235 215481 4.8713 6.2804
Pocillopora_meandrina_HIv1___xfSc0000540 43935 315778 7.1874 9.6945
Pocillopora_meandrina_HIv1___xfSc0000555 43535 249395 5.7286 12.0311
Pocillopora_meandrina_HIv1___xfSc0000565 43357 328720 7.5817 7.2358
Pocillopora_meandrina_HIv1___xfSc0000566 43316 269235 6.2156 8.0242
Pocillopora_meandrina_HIv1___xfSc0000567 43305 141723 3.2727 6.2896
Pocillopora_meandrina_HIv1___xfSc0000570 43295 185998 4.2961 6.6404
Pocillopora_meandrina_HIv1___xfSc0000579 43029 69217 1.6086 3.6479
Pocillopora_meandrina_HIv1___xfSc0000583 42958 246036 5.7274 6.5205
Pocillopora_meandrina_HIv1___xfSc0000596 42675 122492 2.8703 5.1025
Pocillopora_meandrina_HIv1___xfSc0000612 42423 237781 5.605 5.5594
Pocillopora_meandrina_HIv1___xfSc0000616 42355 1918021 45.2844 118.9908
Pocillopora_meandrina_HIv1___xfSc0000621 42164 236577 5.6109 6.936
Pocillopora_meandrina_HIv1___xfSc0000642 41754 184354 4.4152 6.6772
Pocillopora_meandrina_HIv1___xfSc0000655 41446 464729 11.2129 23.4486
Pocillopora_meandrina_HIv1___xfSc0000692 40426 109968 2.7202 4.4267
Pocillopora_meandrina_HIv1___xfSc0000699 40296 42507 1.0549 2.3589
Pocillopora_meandrina_HIv1___xfSc0000704 40233 477933 11.8791 16.2252
Pocillopora_meandrina_HIv1___xfSc0000705 40197 132694 3.3011 5.153
Pocillopora_meandrina_HIv1___xfSc0000716 39998 299655 7.4917 8.4023
Pocillopora_meandrina_HIv1___xfSc0000725 39827 124577 3.128 7.5221
Pocillopora_meandrina_HIv1___xfSc0000729 39775 76914 1.9337 16.2864
Pocillopora_meandrina_HIv1___xfSc0000760 39228 23431 0.5973 1.9665
Pocillopora_meandrina_HIv1___xfSc0000763 39151 304233 7.7708 5.6122
Pocillopora_meandrina_HIv1___xfSc0000765 39117 128753 3.2915 4.3743
Pocillopora_meandrina_HIv1___xfSc0000788 38513 283116 7.3512 7.9172
Pocillopora_meandrina_HIv1___xfSc0000811 37888 261264 6.8957 5.2943
Pocillopora_meandrina_HIv1___xfSc0000812 37881 17963 0.4742 1.0973
Pocillopora_meandrina_HIv1___xfSc0000817 37779 396979 10.5079 7.8351
Pocillopora_meandrina_HIv1___xfSc0000824 37656 187213 4.9717 6.294
Pocillopora_meandrina_HIv1___xfSc0000835 37434 364785 9.7448 8.6677
Pocillopora_meandrina_HIv1___xfSc0000836 37372 169121 4.5253 7.1717
Pocillopora_meandrina_HIv1___xfSc0000837 37368 124835 3.3407 6.0676
Pocillopora_meandrina_HIv1___xfSc0000840 37283 335755 9.0056 13.7014
Pocillopora_meandrina_HIv1___xfSc0000857 37006 54408 1.4702 3.438
Pocillopora_meandrina_HIv1___xfSc0000859 36995 60135 1.6255 3.3812
Pocillopora_meandrina_HIv1___xfSc0000866 36925 122179 3.3088 5.0346
Pocillopora_meandrina_HIv1___xfSc0000868 36831 146618 3.9808 7.7323
Pocillopora_meandrina_HIv1___xfSc0000875 36611 24243 0.6622 1.758
Pocillopora_meandrina_HIv1___xfSc0000885 36416 151564 4.162 6.6289
Pocillopora_meandrina_HIv1___xfSc0000886 36355 202497 5.57 8.9951
Pocillopora_meandrina_HIv1___xfSc0000890 36339 199868 5.5001 10.8052
Pocillopora_meandrina_HIv1___xfSc0000892 36267 26067 0.7188 2.0462
Pocillopora_meandrina_HIv1___xfSc0000943 35168 8611 0.2449 1.0064
Pocillopora_meandrina_HIv1___xfSc0000948 35100 283611 8.0801 8.8461
Pocillopora_meandrina_HIv1___xfSc0000952 34934 108244 3.0985 4.4056
Pocillopora_meandrina_HIv1___xfSc0000953 34905 138534 3.9689 4.9769
Pocillopora_meandrina_HIv1___xfSc0000957 34773 228920 6.5833 10.7172
Pocillopora_meandrina_HIv1___xfSc0000968 34345 39954 1.1633 2.7647
Pocillopora_meandrina_HIv1___xfSc0000974 34140 276523 8.0997 7.2923
Pocillopora_meandrina_HIv1___xfSc0000975 33988 323321 9.5128 10.3291
Pocillopora_meandrina_HIv1___xfSc0000995 33324 100013 3.0012 6.9034
Pocillopora_meandrina_HIv1___xfSc0001011 32918 295587 8.9795 10.7046
Pocillopora_meandrina_HIv1___xfSc0001122 29140 280424 9.6233 11.472
Pocillopora_meandrina_HIv1___xfSc0001170 27381 53311 1.947 3.592
Pocillopora_meandrina_HIv1___xfSc0001179 27200 84329 3.1003 4.9569
Pocillopora_meandrina_HIv1___xfSc0001231 22938 13884 0.6053 1.2225
Pocillopora_meandrina_HIv1___xfSc0001237 22715 82664 3.6392 8.9856
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2754493 6.7467 9.2522
Pocillopora_meandrina_HIv1___xpSc0001275 48561 208646 4.2966 7.3928
Pocillopora_meandrina_HIv1___xpSc0001276 38618 115646 2.9946 5.7166
Pocillopora_meandrina_HIv1___xpSc0001280 35955 188058 5.2304 8.7885
Pocillopora_meandrina_HIv1___xpSc0001281 34238 243921 7.1243 9.5394
Pocillopora_meandrina_HIv1___xpSc0001290 28931 342777 11.8481 8.2469
Pocillopora_meandrina_HIv1___xpSc0001321 15304 34451 2.2511 4.3417
Pocillopora_meandrina_HIv1___xpSc0001331 8958 93240 10.4086 9.4148
Pocillopora_meandrina_HIv1___xpSc0001337 6786 15084 2.2228 4.0951
Pocillopora_meandrina_HIv1___xpSc0001344 5647 34960 6.1909 8.4744
Pocillopora_meandrina_HIv1___xpSc0001355 3576 38139 10.6653 8.2205

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 20:58:46
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