Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-201-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-201-TP2_R1_001.fastp-trim.fq.gz -2 POC-201-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-201-TP2 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 22:34:44 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-201-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 39,030,498
Mapped reads 39,030,498 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 39,030,498 / 100%
Mapped reads, first in pair 19,515,249 / 50%
Mapped reads, second in pair 19,515,249 / 50%
Mapped reads, both in pair 39,030,498 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.43
Overlapping read pairs 11,632,549 / 59.61%
Duplicated reads (estimated) 3,819,216 / 9.79%
Duplication rate 9.48%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,072,111,405 / 40.27%
Number/percentage of C's 503,714,521 / 9.79%
Number/percentage of T's 2,075,126,548 / 40.33%
Number/percentage of G's 494,094,681 / 9.6%
Number/percentage of N's 432,297 / 0.01%
GC Percentage 19.39%

Coverage

Mean 13.7075
Standard Deviation 12.5437
Mean (paired-end reads overlap ignored) 11.68

Mapping Quality

Mean Mapping Quality 22.61

Insert size

Mean 254.21
Standard Deviation 86.78
P25/Median/P75 189 / 247 / 310

Mismatches and indels

General error rate 21.09%
Mismatches 1,065,586,091
Insertions 7,703,190
Mapped reads with at least one insertion 14.74%
Deletions 6,097,786
Mapped reads with at least one deletion 13.1%
Homopolymer indels 52.08%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 328624833 15.1782 11.3646
Pocillopora_meandrina_HIv1___Sc0000001 21507942 329589965 15.3241 10.3359
Pocillopora_meandrina_HIv1___Sc0000002 19741974 301924101 15.2935 10.9747
Pocillopora_meandrina_HIv1___Sc0000003 19417450 256577326 13.2137 12.3142
Pocillopora_meandrina_HIv1___Sc0000004 14584444 197964706 13.5737 22.3152
Pocillopora_meandrina_HIv1___Sc0000005 14098929 206379410 14.6379 9.9734
Pocillopora_meandrina_HIv1___Sc0000006 14068054 206419456 14.6729 11.2611
Pocillopora_meandrina_HIv1___Sc0000007 13590779 192531546 14.1663 11.6578
Pocillopora_meandrina_HIv1___Sc0000008 12446599 190992019 15.3449 10.9313
Pocillopora_meandrina_HIv1___Sc0000009 11983232 102780680 8.577 14.6835
Pocillopora_meandrina_HIv1___Sc0000010 11763137 156841333 13.3333 12.5083
Pocillopora_meandrina_HIv1___Sc0000011 10501528 177280557 16.8814 9.5587
Pocillopora_meandrina_HIv1___Sc0000012 10024633 141687770 14.134 11.8877
Pocillopora_meandrina_HIv1___Sc0000013 9946974 111085221 11.1677 11.223
Pocillopora_meandrina_HIv1___Sc0000014 9536826 148515657 15.5729 10.4316
Pocillopora_meandrina_HIv1___Sc0000015 9393205 134540924 14.3232 10.6072
Pocillopora_meandrina_HIv1___Sc0000016 9288165 132289161 14.2428 11.3582
Pocillopora_meandrina_HIv1___Sc0000017 9274345 130344686 14.0543 10.3849
Pocillopora_meandrina_HIv1___Sc0000018 8584156 126691623 14.7588 10.1429
Pocillopora_meandrina_HIv1___Sc0000019 7112774 99610363 14.0044 11.405
Pocillopora_meandrina_HIv1___Sc0000020 6748058 97958487 14.5165 14.1619
Pocillopora_meandrina_HIv1___Sc0000021 6546105 96839615 14.7935 10.3498
Pocillopora_meandrina_HIv1___Sc0000022 6319256 83261030 13.1758 13.1658
Pocillopora_meandrina_HIv1___Sc0000023 5767069 67200552 11.6525 10.4138
Pocillopora_meandrina_HIv1___Sc0000024 5762297 48466724 8.411 10.2643
Pocillopora_meandrina_HIv1___Sc0000025 5759531 73294880 12.7258 12.2161
Pocillopora_meandrina_HIv1___Sc0000026 5647578 93953877 16.6361 9.2588
Pocillopora_meandrina_HIv1___Sc0000027 5550630 71931329 12.9591 13.7794
Pocillopora_meandrina_HIv1___Sc0000028 5130920 81767032 15.9361 11.5839
Pocillopora_meandrina_HIv1___Sc0000029 4860867 61601152 12.6729 10.3532
Pocillopora_meandrina_HIv1___Sc0000030 4843735 73160747 15.1042 9.7114
Pocillopora_meandrina_HIv1___Sc0000031 4691590 67925805 14.4782 10.231
Pocillopora_meandrina_HIv1___Sc0000032 3615800 58577137 16.2003 11.6511
Pocillopora_meandrina_HIv1___Sc0000033 3306609 35017948 10.5903 10.9662
Pocillopora_meandrina_HIv1___Sc0000034 3122802 48328790 15.4761 10.8033
Pocillopora_meandrina_HIv1___Sc0000035 3015365 34905454 11.5759 11.6439
Pocillopora_meandrina_HIv1___Sc0000036 3007169 52927844 17.6006 11.0869
Pocillopora_meandrina_HIv1___Sc0000037 2860435 43829777 15.3228 21.4531
Pocillopora_meandrina_HIv1___Sc0000038 2701138 34795024 12.8816 11.7666
Pocillopora_meandrina_HIv1___Sc0000039 2599273 28447836 10.9445 10.2473
Pocillopora_meandrina_HIv1___Sc0000040 2445666 32120255 13.1335 12.5381
Pocillopora_meandrina_HIv1___Sc0000041 2159376 32855566 15.2153 10.1476
Pocillopora_meandrina_HIv1___Sc0000042 1957488 24995775 12.7693 10.817
Pocillopora_meandrina_HIv1___Sc0000043 1845599 23732679 12.8591 10.6568
Pocillopora_meandrina_HIv1___Sc0000044 1724711 25631025 14.8611 11.7032
Pocillopora_meandrina_HIv1___Sc0000045 1153740 14793748 12.8224 10.3945
Pocillopora_meandrina_HIv1___Sc0000046 755410 7218807 9.5561 11.692
Pocillopora_meandrina_HIv1___Sc0000047 239089 377645 1.5795 4.2379
Pocillopora_meandrina_HIv1___Sc0000048 214660 45066 0.2099 1.4046
Pocillopora_meandrina_HIv1___Sc0000049 179266 870971 4.8585 10.6122
Pocillopora_meandrina_HIv1___Sc0000050 177168 162762 0.9187 2.4237
Pocillopora_meandrina_HIv1___Sc0000051 165057 1175199 7.12 10.7777
Pocillopora_meandrina_HIv1___Sc0000052 155210 102772 0.6621 7.913
Pocillopora_meandrina_HIv1___Sc0000053 123249 311011 2.5234 5.9674
Pocillopora_meandrina_HIv1___Sc0000054 122643 1400947 11.423 12.4079
Pocillopora_meandrina_HIv1___Sc0000055 121609 456434 3.7533 7.4065
Pocillopora_meandrina_HIv1___Sc0000056 112816 45701 0.4051 3.8383
Pocillopora_meandrina_HIv1___Sc0000057 107171 348215 3.2492 8.25
Pocillopora_meandrina_HIv1___Sc0000058 98341 50083 0.5093 4.1816
Pocillopora_meandrina_HIv1___Sc0000059 83292 36298 0.4358 6.0613
Pocillopora_meandrina_HIv1___Sc0000060 79483 268 0.0034 0.0728
Pocillopora_meandrina_HIv1___Sc0000061 75390 770682 10.2226 26.1886
Pocillopora_meandrina_HIv1___Sc0000062 74194 12247 0.1651 0.7243
Pocillopora_meandrina_HIv1___Sc0000063 73457 159400 2.17 21.3609
Pocillopora_meandrina_HIv1___Sc0000064 72700 17311 0.2381 1.1406
Pocillopora_meandrina_HIv1___Sc0000065 67986 11486 0.1689 1.837
Pocillopora_meandrina_HIv1___Sc0000066 66659 415232 6.2292 6.6198
Pocillopora_meandrina_HIv1___Sc0000067 64947 97945 1.5081 3.6275
Pocillopora_meandrina_HIv1___Sc0000068 64340 6880 0.1069 0.7188
Pocillopora_meandrina_HIv1___Sc0000069 62616 163084 2.6045 6.9458
Pocillopora_meandrina_HIv1___Sc0000070 60121 258420 4.2983 24.2482
Pocillopora_meandrina_HIv1___Sc0000071 57157 59723 1.0449 2.2405
Pocillopora_meandrina_HIv1___Sc0000072 56626 9863 0.1742 2.0395
Pocillopora_meandrina_HIv1___Sc0000073 56082 11999 0.214 0.7853
Pocillopora_meandrina_HIv1___Sc0000074 55210 536 0.0097 0.1071
Pocillopora_meandrina_HIv1___Sc0000075 54685 775 0.0142 0.1462
Pocillopora_meandrina_HIv1___Sc0000076 54587 147670 2.7052 13.449
Pocillopora_meandrina_HIv1___Sc0000077 53379 20674 0.3873 0.8948
Pocillopora_meandrina_HIv1___Sc0000078 51564 788 0.0153 0.1755
Pocillopora_meandrina_HIv1___Sc0000079 49664 1324 0.0267 0.1983
Pocillopora_meandrina_HIv1___Sc0000080 47218 92290 1.9546 5.3407
Pocillopora_meandrina_HIv1___Sc0000081 42490 9461 0.2227 0.5952
Pocillopora_meandrina_HIv1___Sc0000082 32657 1147298 35.1318 83.6261
Pocillopora_meandrina_HIv1___Sc0000083 27992 2921 0.1044 0.4317
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 14408421 8.9962 14.3
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4224710 3.5273 6.6464
Pocillopora_meandrina_HIv1___xfSc0000002 779520 9532244 12.2284 16.245
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1493078 3.2293 5.9571
Pocillopora_meandrina_HIv1___xfSc0000004 334777 820310 2.4503 4.6243
Pocillopora_meandrina_HIv1___xfSc0000006 290100 571180 1.9689 3.8578
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1199679 4.7558 6.6682
Pocillopora_meandrina_HIv1___xfSc0000012 148278 878390 5.9239 9.6324
Pocillopora_meandrina_HIv1___xfSc0000014 118081 20518 0.1738 0.7527
Pocillopora_meandrina_HIv1___xfSc0000017 98555 673295 6.8317 96.1688
Pocillopora_meandrina_HIv1___xfSc0000021 95778 681770 7.1182 11.5065
Pocillopora_meandrina_HIv1___xfSc0000024 90744 930647 10.2557 13.7708
Pocillopora_meandrina_HIv1___xfSc0000029 85532 175130 2.0475 5.477
Pocillopora_meandrina_HIv1___xfSc0000038 77395 18391 0.2376 1.6533
Pocillopora_meandrina_HIv1___xfSc0000058 69718 418730 6.0061 9.9275
Pocillopora_meandrina_HIv1___xfSc0000059 69426 184141 2.6523 7.5477
Pocillopora_meandrina_HIv1___xfSc0000074 66573 146517 2.2008 4.1442
Pocillopora_meandrina_HIv1___xfSc0000081 65415 306307 4.6825 5.6974
Pocillopora_meandrina_HIv1___xfSc0000083 65317 858990 13.1511 14.6478
Pocillopora_meandrina_HIv1___xfSc0000092 63607 546507 8.5919 7.8918
Pocillopora_meandrina_HIv1___xfSc0000094 62842 35483 0.5646 1.6012
Pocillopora_meandrina_HIv1___xfSc0000113 60556 775504 12.8064 14.2235
Pocillopora_meandrina_HIv1___xfSc0000132 59032 54523 0.9236 2.4786
Pocillopora_meandrina_HIv1___xfSc0000145 58221 68341 1.1738 3.3804
Pocillopora_meandrina_HIv1___xfSc0000146 58151 114161 1.9632 4.339
Pocillopora_meandrina_HIv1___xfSc0000168 56681 292578 5.1618 8.3108
Pocillopora_meandrina_HIv1___xfSc0000175 56271 139412 2.4775 7.0077
Pocillopora_meandrina_HIv1___xfSc0000195 55223 9012 0.1632 0.8305
Pocillopora_meandrina_HIv1___xfSc0000199 55095 199369 3.6186 7.5752
Pocillopora_meandrina_HIv1___xfSc0000205 54658 243238 4.4502 6.9876
Pocillopora_meandrina_HIv1___xfSc0000206 54623 193690 3.5459 5.3718
Pocillopora_meandrina_HIv1___xfSc0000212 54299 303507 5.5896 8.3691
Pocillopora_meandrina_HIv1___xfSc0000217 54168 466449 8.6112 17.4949
Pocillopora_meandrina_HIv1___xfSc0000223 53823 318236 5.9126 6.5469
Pocillopora_meandrina_HIv1___xfSc0000228 53382 302644 5.6694 20.13
Pocillopora_meandrina_HIv1___xfSc0000237 53049 249384 4.701 6.3066
Pocillopora_meandrina_HIv1___xfSc0000262 52308 438764 8.3881 8.4165
Pocillopora_meandrina_HIv1___xfSc0000264 52264 981617 18.7819 16.2656
Pocillopora_meandrina_HIv1___xfSc0000272 52107 258838 4.9674 6.838
Pocillopora_meandrina_HIv1___xfSc0000275 51938 193431 3.7243 5.8343
Pocillopora_meandrina_HIv1___xfSc0000284 51483 351726 6.8319 9.5348
Pocillopora_meandrina_HIv1___xfSc0000288 51367 219038 4.2642 12.1363
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9473 0.1863 0.7028
Pocillopora_meandrina_HIv1___xfSc0000301 50809 466635 9.1841 10.16
Pocillopora_meandrina_HIv1___xfSc0000343 49544 250648 5.0591 7.5069
Pocillopora_meandrina_HIv1___xfSc0000376 48519 281413 5.8001 15.7148
Pocillopora_meandrina_HIv1___xfSc0000415 47398 179215 3.7811 5.1721
Pocillopora_meandrina_HIv1___xfSc0000423 47202 51250 1.0858 2.3685
Pocillopora_meandrina_HIv1___xfSc0000426 47096 703323 14.9338 17.0803
Pocillopora_meandrina_HIv1___xfSc0000428 47057 359317 7.6358 12.5437
Pocillopora_meandrina_HIv1___xfSc0000436 46816 302695 6.4656 12.633
Pocillopora_meandrina_HIv1___xfSc0000445 46561 73150 1.5711 3.8133
Pocillopora_meandrina_HIv1___xfSc0000447 46542 332293 7.1396 8.6598
Pocillopora_meandrina_HIv1___xfSc0000469 45938 309376 6.7346 6.2238
Pocillopora_meandrina_HIv1___xfSc0000477 45781 269915 5.8958 6.4774
Pocillopora_meandrina_HIv1___xfSc0000479 45736 157129 3.4356 5.5939
Pocillopora_meandrina_HIv1___xfSc0000482 45585 710002 15.5753 24.8801
Pocillopora_meandrina_HIv1___xfSc0000488 45379 228659 5.0389 6.6801
Pocillopora_meandrina_HIv1___xfSc0000506 44781 108741 2.4283 4.1513
Pocillopora_meandrina_HIv1___xfSc0000527 44235 210800 4.7655 6.8624
Pocillopora_meandrina_HIv1___xfSc0000540 43935 332802 7.5749 11.6553
Pocillopora_meandrina_HIv1___xfSc0000555 43535 213040 4.8935 12.7257
Pocillopora_meandrina_HIv1___xfSc0000565 43357 251347 5.7971 5.6425
Pocillopora_meandrina_HIv1___xfSc0000566 43316 236111 5.4509 9.1839
Pocillopora_meandrina_HIv1___xfSc0000567 43305 130109 3.0045 5.4491
Pocillopora_meandrina_HIv1___xfSc0000570 43295 70334 1.6245 3.9956
Pocillopora_meandrina_HIv1___xfSc0000579 43029 68605 1.5944 3.5119
Pocillopora_meandrina_HIv1___xfSc0000583 42958 277887 6.4688 6.9351
Pocillopora_meandrina_HIv1___xfSc0000596 42675 224553 5.2619 8.8035
Pocillopora_meandrina_HIv1___xfSc0000612 42423 87334 2.0586 3.6897
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2612930 61.6912 176.9783
Pocillopora_meandrina_HIv1___xfSc0000621 42164 283830 6.7316 8.024
Pocillopora_meandrina_HIv1___xfSc0000642 41754 159298 3.8152 5.6702
Pocillopora_meandrina_HIv1___xfSc0000655 41446 719292 17.3549 35.403
Pocillopora_meandrina_HIv1___xfSc0000692 40426 177624 4.3938 5.4921
Pocillopora_meandrina_HIv1___xfSc0000699 40296 30822 0.7649 1.9243
Pocillopora_meandrina_HIv1___xfSc0000704 40233 380022 9.4455 11.8255
Pocillopora_meandrina_HIv1___xfSc0000705 40197 97919 2.436 5.0105
Pocillopora_meandrina_HIv1___xfSc0000716 39998 289540 7.2389 8.7205
Pocillopora_meandrina_HIv1___xfSc0000725 39827 70589 1.7724 5.9349
Pocillopora_meandrina_HIv1___xfSc0000729 39775 16643 0.4184 2.9658
Pocillopora_meandrina_HIv1___xfSc0000760 39228 11919 0.3038 1.4711
Pocillopora_meandrina_HIv1___xfSc0000763 39151 234017 5.9773 6.4007
Pocillopora_meandrina_HIv1___xfSc0000765 39117 68352 1.7474 5.3538
Pocillopora_meandrina_HIv1___xfSc0000788 38513 388800 10.0953 17.9485
Pocillopora_meandrina_HIv1___xfSc0000811 37888 154203 4.07 6.0423
Pocillopora_meandrina_HIv1___xfSc0000812 37881 24796 0.6546 1.313
Pocillopora_meandrina_HIv1___xfSc0000817 37779 151984 4.023 4.3545
Pocillopora_meandrina_HIv1___xfSc0000824 37656 130678 3.4703 5.4325
Pocillopora_meandrina_HIv1___xfSc0000835 37434 261173 6.9769 8.6757
Pocillopora_meandrina_HIv1___xfSc0000836 37372 263348 7.0467 11.0155
Pocillopora_meandrina_HIv1___xfSc0000837 37368 492115 13.1694 15.1521
Pocillopora_meandrina_HIv1___xfSc0000840 37283 336698 9.0309 9.686
Pocillopora_meandrina_HIv1___xfSc0000857 37006 119164 3.2201 3.9607
Pocillopora_meandrina_HIv1___xfSc0000859 36995 60189 1.6269 3.158
Pocillopora_meandrina_HIv1___xfSc0000866 36925 32391 0.8772 2.0428
Pocillopora_meandrina_HIv1___xfSc0000868 36831 130584 3.5455 7.0941
Pocillopora_meandrina_HIv1___xfSc0000875 36611 28022 0.7654 2.5019
Pocillopora_meandrina_HIv1___xfSc0000885 36416 179439 4.9275 7.4776
Pocillopora_meandrina_HIv1___xfSc0000886 36355 100167 2.7552 6.6498
Pocillopora_meandrina_HIv1___xfSc0000890 36339 185216 5.0969 9.4195
Pocillopora_meandrina_HIv1___xfSc0000892 36267 146149 4.0298 19.7445
Pocillopora_meandrina_HIv1___xfSc0000943 35168 6198 0.1762 0.6701
Pocillopora_meandrina_HIv1___xfSc0000948 35100 192505 5.4845 7.7767
Pocillopora_meandrina_HIv1___xfSc0000952 34934 392142 11.2252 9.9895
Pocillopora_meandrina_HIv1___xfSc0000953 34905 149400 4.2802 5.9334
Pocillopora_meandrina_HIv1___xfSc0000957 34773 104086 2.9933 5.1008
Pocillopora_meandrina_HIv1___xfSc0000968 34345 16746 0.4876 1.9316
Pocillopora_meandrina_HIv1___xfSc0000974 34140 204731 5.9968 5.91
Pocillopora_meandrina_HIv1___xfSc0000975 33988 219679 6.4634 6.7615
Pocillopora_meandrina_HIv1___xfSc0000995 33324 108143 3.2452 6.4798
Pocillopora_meandrina_HIv1___xfSc0001011 32918 179406 5.4501 12.9202
Pocillopora_meandrina_HIv1___xfSc0001122 29140 214888 7.3743 10.1285
Pocillopora_meandrina_HIv1___xfSc0001170 27381 10751 0.3926 1.336
Pocillopora_meandrina_HIv1___xfSc0001179 27200 73602 2.706 4.5885
Pocillopora_meandrina_HIv1___xfSc0001231 22938 11816 0.5151 1.0317
Pocillopora_meandrina_HIv1___xfSc0001237 22715 79457 3.498 9.1902
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2411362 5.9063 9.9454
Pocillopora_meandrina_HIv1___xpSc0001275 48561 163702 3.3711 6.7594
Pocillopora_meandrina_HIv1___xpSc0001276 38618 91604 2.3721 5.0595
Pocillopora_meandrina_HIv1___xpSc0001280 35955 230868 6.421 8.9227
Pocillopora_meandrina_HIv1___xpSc0001281 34238 146725 4.2854 6.6941
Pocillopora_meandrina_HIv1___xpSc0001290 28931 105426 3.644 4.8046
Pocillopora_meandrina_HIv1___xpSc0001321 15304 62811 4.1042 6.6841
Pocillopora_meandrina_HIv1___xpSc0001331 8958 153699 17.1577 8.7384
Pocillopora_meandrina_HIv1___xpSc0001337 6786 16776 2.4721 5.3429
Pocillopora_meandrina_HIv1___xpSc0001344 5647 45108 7.988 10.3173
Pocillopora_meandrina_HIv1___xpSc0001355 3576 39505 11.0473 7.8617

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 22:34:45
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