Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-57-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-57-TP3_R1_001.fastp-trim.fq.gz -2 POC-57-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-57-TP3 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:18:48 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-57-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 49,493,974
Mapped reads 49,493,974 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 49,493,974 / 100%
Mapped reads, first in pair 24,746,987 / 50%
Mapped reads, second in pair 24,746,987 / 50%
Mapped reads, both in pair 49,493,974 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.29
Overlapping read pairs 15,599,006 / 63.03%
Duplicated reads (estimated) 6,172,013 / 12.47%
Duplication rate 12.11%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,602,938,934 / 40.23%
Number/percentage of C's 636,828,086 / 9.84%
Number/percentage of T's 2,605,630,292 / 40.28%
Number/percentage of G's 623,483,350 / 9.64%
Number/percentage of N's 542,361 / 0.01%
GC Percentage 19.48%

Coverage

Mean 17.234
Standard Deviation 14.6806
Mean (paired-end reads overlap ignored) 14.39

Mapping Quality

Mean Mapping Quality 22.69

Insert size

Mean 244.74
Standard Deviation 88.08
P25/Median/P75 176 / 238 / 301

Mismatches and indels

General error rate 21.17%
Mismatches 1,345,389,219
Insertions 9,556,138
Mapped reads with at least one insertion 14.51%
Deletions 7,621,642
Mapped reads with at least one deletion 12.93%
Homopolymer indels 52.15%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 401679634 18.5524 13.1003
Pocillopora_meandrina_HIv1___Sc0000001 21507942 419373282 19.4985 12.9328
Pocillopora_meandrina_HIv1___Sc0000002 19741974 376074534 19.0495 12.8184
Pocillopora_meandrina_HIv1___Sc0000003 19417450 327907406 16.8873 14.0981
Pocillopora_meandrina_HIv1___Sc0000004 14584444 245349334 16.8227 20.1182
Pocillopora_meandrina_HIv1___Sc0000005 14098929 261806136 18.5692 12.4899
Pocillopora_meandrina_HIv1___Sc0000006 14068054 259792620 18.4668 14.0455
Pocillopora_meandrina_HIv1___Sc0000007 13590779 246496112 18.137 14.6017
Pocillopora_meandrina_HIv1___Sc0000008 12446599 245114367 19.6933 13.6786
Pocillopora_meandrina_HIv1___Sc0000009 11983232 140881426 11.7565 17.1621
Pocillopora_meandrina_HIv1___Sc0000010 11763137 200262060 17.0245 15.0095
Pocillopora_meandrina_HIv1___Sc0000011 10501528 215638894 20.534 11.247
Pocillopora_meandrina_HIv1___Sc0000012 10024633 179976446 17.9534 14.8076
Pocillopora_meandrina_HIv1___Sc0000013 9946974 140791312 14.1542 13.6668
Pocillopora_meandrina_HIv1___Sc0000014 9536826 185177401 19.4171 12.8584
Pocillopora_meandrina_HIv1___Sc0000015 9393205 163511409 17.4074 12.6026
Pocillopora_meandrina_HIv1___Sc0000016 9288165 162163447 17.4591 13.4602
Pocillopora_meandrina_HIv1___Sc0000017 9274345 162083526 17.4765 13.3604
Pocillopora_meandrina_HIv1___Sc0000018 8584156 161263989 18.7862 12.8131
Pocillopora_meandrina_HIv1___Sc0000019 7112774 126992471 17.8541 14.04
Pocillopora_meandrina_HIv1___Sc0000020 6748058 132140837 19.5821 20.2336
Pocillopora_meandrina_HIv1___Sc0000021 6546105 126850889 19.3781 13.4034
Pocillopora_meandrina_HIv1___Sc0000022 6319256 105477755 16.6915 16.358
Pocillopora_meandrina_HIv1___Sc0000023 5767069 85867241 14.8892 13.5501
Pocillopora_meandrina_HIv1___Sc0000024 5762297 68219372 11.8389 13.6151
Pocillopora_meandrina_HIv1___Sc0000025 5759531 86853483 15.08 15.1035
Pocillopora_meandrina_HIv1___Sc0000026 5647578 119733947 21.2009 12.9194
Pocillopora_meandrina_HIv1___Sc0000027 5550630 90522626 16.3085 17.9528
Pocillopora_meandrina_HIv1___Sc0000028 5130920 105785714 20.6173 16.1009
Pocillopora_meandrina_HIv1___Sc0000029 4860867 76749094 15.7892 12.942
Pocillopora_meandrina_HIv1___Sc0000030 4843735 90326715 18.6482 12.3043
Pocillopora_meandrina_HIv1___Sc0000031 4691590 83735139 17.8479 12.3639
Pocillopora_meandrina_HIv1___Sc0000032 3615800 72152347 19.9547 14.1951
Pocillopora_meandrina_HIv1___Sc0000033 3306609 42982060 12.9988 13.1832
Pocillopora_meandrina_HIv1___Sc0000034 3122802 58443573 18.7151 13.3168
Pocillopora_meandrina_HIv1___Sc0000035 3015365 47020788 15.5937 15.8627
Pocillopora_meandrina_HIv1___Sc0000036 3007169 61133632 20.3293 11.5997
Pocillopora_meandrina_HIv1___Sc0000037 2860435 53257691 18.6187 15.7549
Pocillopora_meandrina_HIv1___Sc0000038 2701138 47174305 17.4646 14.564
Pocillopora_meandrina_HIv1___Sc0000039 2599273 37336562 14.3642 14.0423
Pocillopora_meandrina_HIv1___Sc0000040 2445666 41207185 16.8491 15.4626
Pocillopora_meandrina_HIv1___Sc0000041 2159376 40811116 18.8995 12.2215
Pocillopora_meandrina_HIv1___Sc0000042 1957488 29733096 15.1894 12.7317
Pocillopora_meandrina_HIv1___Sc0000043 1845599 26835578 14.5403 12.4642
Pocillopora_meandrina_HIv1___Sc0000044 1724711 31198812 18.0893 13.3044
Pocillopora_meandrina_HIv1___Sc0000045 1153740 17921751 15.5336 14.1105
Pocillopora_meandrina_HIv1___Sc0000046 755410 8689868 11.5035 14.4216
Pocillopora_meandrina_HIv1___Sc0000047 239089 348389 1.4572 4.4102
Pocillopora_meandrina_HIv1___Sc0000048 214660 45729 0.213 1.25
Pocillopora_meandrina_HIv1___Sc0000049 179266 258827 1.4438 6.4296
Pocillopora_meandrina_HIv1___Sc0000050 177168 220907 1.2469 3.7415
Pocillopora_meandrina_HIv1___Sc0000051 165057 792182 4.7994 8.0026
Pocillopora_meandrina_HIv1___Sc0000052 155210 93861 0.6047 7.1505
Pocillopora_meandrina_HIv1___Sc0000053 123249 240311 1.9498 4.7574
Pocillopora_meandrina_HIv1___Sc0000054 122643 1830753 14.9275 15.4707
Pocillopora_meandrina_HIv1___Sc0000055 121609 445732 3.6653 7.7326
Pocillopora_meandrina_HIv1___Sc0000056 112816 59683 0.529 5.2448
Pocillopora_meandrina_HIv1___Sc0000057 107171 539454 5.0336 10.4692
Pocillopora_meandrina_HIv1___Sc0000058 98341 97746 0.9939 11.7681
Pocillopora_meandrina_HIv1___Sc0000059 83292 2676 0.0321 0.2327
Pocillopora_meandrina_HIv1___Sc0000060 79483 0 0 0
Pocillopora_meandrina_HIv1___Sc0000061 75390 185360 2.4587 5.972
Pocillopora_meandrina_HIv1___Sc0000062 74194 13689 0.1845 0.9091
Pocillopora_meandrina_HIv1___Sc0000063 73457 16545 0.2252 2.0194
Pocillopora_meandrina_HIv1___Sc0000064 72700 2607 0.0359 0.2429
Pocillopora_meandrina_HIv1___Sc0000065 67986 5836 0.0858 0.5467
Pocillopora_meandrina_HIv1___Sc0000066 66659 509526 7.6438 8.2756
Pocillopora_meandrina_HIv1___Sc0000067 64947 120317 1.8525 4.0222
Pocillopora_meandrina_HIv1___Sc0000068 64340 8457 0.1314 0.8614
Pocillopora_meandrina_HIv1___Sc0000069 62616 210655 3.3642 8.6636
Pocillopora_meandrina_HIv1___Sc0000070 60121 268171 4.4605 25.3578
Pocillopora_meandrina_HIv1___Sc0000071 57157 61530 1.0765 2.3085
Pocillopora_meandrina_HIv1___Sc0000072 56626 14635 0.2585 2.9111
Pocillopora_meandrina_HIv1___Sc0000073 56082 12539 0.2236 0.8124
Pocillopora_meandrina_HIv1___Sc0000074 55210 270 0.0049 0.0921
Pocillopora_meandrina_HIv1___Sc0000075 54685 1608 0.0294 0.4207
Pocillopora_meandrina_HIv1___Sc0000076 54587 218839 4.009 19.6243
Pocillopora_meandrina_HIv1___Sc0000077 53379 22121 0.4144 0.9871
Pocillopora_meandrina_HIv1___Sc0000078 51564 524 0.0102 0.1278
Pocillopora_meandrina_HIv1___Sc0000079 49664 541 0.0109 0.1037
Pocillopora_meandrina_HIv1___Sc0000080 47218 103517 2.1923 5.639
Pocillopora_meandrina_HIv1___Sc0000081 42490 9163 0.2157 0.7393
Pocillopora_meandrina_HIv1___Sc0000082 32657 619468 18.9689 40.6165
Pocillopora_meandrina_HIv1___Sc0000083 27992 7498 0.2679 1.0272
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 8339725 5.2071 9.541
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 6999824 5.8443 11.0732
Pocillopora_meandrina_HIv1___xfSc0000002 779520 7860847 10.0842 13.4282
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2447022 5.2926 9.8069
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1150105 3.4354 6.3553
Pocillopora_meandrina_HIv1___xfSc0000006 290100 753279 2.5966 5.3188
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2311449 9.163 11.9435
Pocillopora_meandrina_HIv1___xfSc0000012 148278 611420 4.1235 9.6058
Pocillopora_meandrina_HIv1___xfSc0000014 118081 23287 0.1972 0.8417
Pocillopora_meandrina_HIv1___xfSc0000017 98555 451801 4.5843 69.7302
Pocillopora_meandrina_HIv1___xfSc0000021 95778 706201 7.3733 13.0697
Pocillopora_meandrina_HIv1___xfSc0000024 90744 615056 6.7779 11.0049
Pocillopora_meandrina_HIv1___xfSc0000029 85532 228723 2.6741 7.0457
Pocillopora_meandrina_HIv1___xfSc0000038 77395 46007 0.5944 5.3452
Pocillopora_meandrina_HIv1___xfSc0000058 69718 511294 7.3337 11.0514
Pocillopora_meandrina_HIv1___xfSc0000059 69426 499012 7.1877 11.1692
Pocillopora_meandrina_HIv1___xfSc0000074 66573 302029 4.5368 7.5534
Pocillopora_meandrina_HIv1___xfSc0000081 65415 234234 3.5807 5.9481
Pocillopora_meandrina_HIv1___xfSc0000083 65317 856679 13.1157 12.2922
Pocillopora_meandrina_HIv1___xfSc0000092 63607 587177 9.2313 10.8208
Pocillopora_meandrina_HIv1___xfSc0000094 62842 102431 1.63 4.2091
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1145599 18.918 21.9124
Pocillopora_meandrina_HIv1___xfSc0000132 59032 41876 0.7094 2.1789
Pocillopora_meandrina_HIv1___xfSc0000145 58221 660273 11.3408 10.1898
Pocillopora_meandrina_HIv1___xfSc0000146 58151 156274 2.6874 6.4835
Pocillopora_meandrina_HIv1___xfSc0000168 56681 360276 6.3562 9.7893
Pocillopora_meandrina_HIv1___xfSc0000175 56271 265396 4.7164 11.9001
Pocillopora_meandrina_HIv1___xfSc0000195 55223 8159 0.1477 1.2519
Pocillopora_meandrina_HIv1___xfSc0000199 55095 871856 15.8246 25.0361
Pocillopora_meandrina_HIv1___xfSc0000205 54658 356505 6.5225 12.1912
Pocillopora_meandrina_HIv1___xfSc0000206 54623 240053 4.3947 6.8298
Pocillopora_meandrina_HIv1___xfSc0000212 54299 380302 7.0038 10.6345
Pocillopora_meandrina_HIv1___xfSc0000217 54168 391370 7.2251 17.6715
Pocillopora_meandrina_HIv1___xfSc0000223 53823 441555 8.2038 9.62
Pocillopora_meandrina_HIv1___xfSc0000228 53382 554607 10.3894 37.0475
Pocillopora_meandrina_HIv1___xfSc0000237 53049 282151 5.3187 7.8958
Pocillopora_meandrina_HIv1___xfSc0000262 52308 211015 4.0341 6.5031
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1409955 26.9776 25.481
Pocillopora_meandrina_HIv1___xfSc0000272 52107 340257 6.53 9.6685
Pocillopora_meandrina_HIv1___xfSc0000275 51938 194780 3.7502 7.3699
Pocillopora_meandrina_HIv1___xfSc0000284 51483 489829 9.5144 11.6189
Pocillopora_meandrina_HIv1___xfSc0000288 51367 902334 17.5664 19.6273
Pocillopora_meandrina_HIv1___xfSc0000300 50845 10591 0.2083 0.7447
Pocillopora_meandrina_HIv1___xfSc0000301 50809 484866 9.5429 9.8854
Pocillopora_meandrina_HIv1___xfSc0000343 49544 172877 3.4894 6.5104
Pocillopora_meandrina_HIv1___xfSc0000376 48519 429205 8.8461 25.1633
Pocillopora_meandrina_HIv1___xfSc0000415 47398 469649 9.9086 11.8356
Pocillopora_meandrina_HIv1___xfSc0000423 47202 48697 1.0317 2.8022
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1602323 34.0225 37.2898
Pocillopora_meandrina_HIv1___xfSc0000428 47057 475280 10.1001 21.6273
Pocillopora_meandrina_HIv1___xfSc0000436 46816 467986 9.9963 21.7529
Pocillopora_meandrina_HIv1___xfSc0000445 46561 88300 1.8964 4.4025
Pocillopora_meandrina_HIv1___xfSc0000447 46542 290659 6.2451 8.1716
Pocillopora_meandrina_HIv1___xfSc0000469 45938 427366 9.3031 9.2521
Pocillopora_meandrina_HIv1___xfSc0000477 45781 522244 11.4074 14.8824
Pocillopora_meandrina_HIv1___xfSc0000479 45736 188646 4.1247 6.7191
Pocillopora_meandrina_HIv1___xfSc0000482 45585 924750 20.2863 31.052
Pocillopora_meandrina_HIv1___xfSc0000488 45379 336613 7.4178 10.7514
Pocillopora_meandrina_HIv1___xfSc0000506 44781 199145 4.4471 6.5447
Pocillopora_meandrina_HIv1___xfSc0000527 44235 304275 6.8786 10.4172
Pocillopora_meandrina_HIv1___xfSc0000540 43935 330681 7.5266 9.3237
Pocillopora_meandrina_HIv1___xfSc0000555 43535 237773 5.4617 9.7325
Pocillopora_meandrina_HIv1___xfSc0000565 43357 381036 8.7883 8.9197
Pocillopora_meandrina_HIv1___xfSc0000566 43316 255205 5.8917 8.471
Pocillopora_meandrina_HIv1___xfSc0000567 43305 196615 4.5402 8.8164
Pocillopora_meandrina_HIv1___xfSc0000570 43295 108451 2.5049 6.2312
Pocillopora_meandrina_HIv1___xfSc0000579 43029 66940 1.5557 3.7904
Pocillopora_meandrina_HIv1___xfSc0000583 42958 336968 7.8441 8.6384
Pocillopora_meandrina_HIv1___xfSc0000596 42675 235741 5.5241 10.4492
Pocillopora_meandrina_HIv1___xfSc0000612 42423 135683 3.1983 5.3906
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2623100 61.9313 177.5982
Pocillopora_meandrina_HIv1___xfSc0000621 42164 453914 10.7654 11.776
Pocillopora_meandrina_HIv1___xfSc0000642 41754 140961 3.376 6.3933
Pocillopora_meandrina_HIv1___xfSc0000655 41446 261088 6.2995 12.9568
Pocillopora_meandrina_HIv1___xfSc0000692 40426 437748 10.8284 12.7334
Pocillopora_meandrina_HIv1___xfSc0000699 40296 35744 0.887 2.3103
Pocillopora_meandrina_HIv1___xfSc0000704 40233 589235 14.6456 18.7182
Pocillopora_meandrina_HIv1___xfSc0000705 40197 146429 3.6428 6.9474
Pocillopora_meandrina_HIv1___xfSc0000716 39998 208903 5.2228 7.7396
Pocillopora_meandrina_HIv1___xfSc0000725 39827 98425 2.4713 7.1525
Pocillopora_meandrina_HIv1___xfSc0000729 39775 22733 0.5715 4.4903
Pocillopora_meandrina_HIv1___xfSc0000760 39228 9101 0.232 1.3382
Pocillopora_meandrina_HIv1___xfSc0000763 39151 297609 7.6016 7.7028
Pocillopora_meandrina_HIv1___xfSc0000765 39117 119826 3.0633 7.4631
Pocillopora_meandrina_HIv1___xfSc0000788 38513 335305 8.7063 10.9229
Pocillopora_meandrina_HIv1___xfSc0000811 37888 602956 15.9142 15.578
Pocillopora_meandrina_HIv1___xfSc0000812 37881 28914 0.7633 1.3206
Pocillopora_meandrina_HIv1___xfSc0000817 37779 433132 11.4649 10.8323
Pocillopora_meandrina_HIv1___xfSc0000824 37656 275578 7.3183 12.0641
Pocillopora_meandrina_HIv1___xfSc0000835 37434 139380 3.7234 6.1164
Pocillopora_meandrina_HIv1___xfSc0000836 37372 222586 5.956 11.013
Pocillopora_meandrina_HIv1___xfSc0000837 37368 364846 9.7636 8.5591
Pocillopora_meandrina_HIv1___xfSc0000840 37283 333892 8.9556 16.3743
Pocillopora_meandrina_HIv1___xfSc0000857 37006 209113 5.6508 7.6881
Pocillopora_meandrina_HIv1___xfSc0000859 36995 45159 1.2207 3.2323
Pocillopora_meandrina_HIv1___xfSc0000866 36925 78869 2.1359 3.614
Pocillopora_meandrina_HIv1___xfSc0000868 36831 124764 3.3875 6.4215
Pocillopora_meandrina_HIv1___xfSc0000875 36611 30756 0.8401 2.3795
Pocillopora_meandrina_HIv1___xfSc0000885 36416 362182 9.9457 14.7037
Pocillopora_meandrina_HIv1___xfSc0000886 36355 169129 4.6522 9.8703
Pocillopora_meandrina_HIv1___xfSc0000890 36339 236928 6.5199 9.4017
Pocillopora_meandrina_HIv1___xfSc0000892 36267 178564 4.9236 25.2209
Pocillopora_meandrina_HIv1___xfSc0000943 35168 11819 0.3361 1.5254
Pocillopora_meandrina_HIv1___xfSc0000948 35100 235060 6.6969 9.653
Pocillopora_meandrina_HIv1___xfSc0000952 34934 101969 2.9189 6.4935
Pocillopora_meandrina_HIv1___xfSc0000953 34905 192780 5.523 6.8891
Pocillopora_meandrina_HIv1___xfSc0000957 34773 268858 7.7318 13.328
Pocillopora_meandrina_HIv1___xfSc0000968 34345 17295 0.5036 1.8252
Pocillopora_meandrina_HIv1___xfSc0000974 34140 278263 8.1506 9.3106
Pocillopora_meandrina_HIv1___xfSc0000975 33988 352821 10.3808 9.5759
Pocillopora_meandrina_HIv1___xfSc0000995 33324 113814 3.4154 9.0146
Pocillopora_meandrina_HIv1___xfSc0001011 32918 320944 9.7498 21.8968
Pocillopora_meandrina_HIv1___xfSc0001122 29140 488193 16.7534 13.1
Pocillopora_meandrina_HIv1___xfSc0001170 27381 24089 0.8798 2.3499
Pocillopora_meandrina_HIv1___xfSc0001179 27200 95982 3.5288 6.5861
Pocillopora_meandrina_HIv1___xfSc0001231 22938 13139 0.5728 1.1356
Pocillopora_meandrina_HIv1___xfSc0001237 22715 78063 3.4366 8.6587
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3278887 8.0312 13.1868
Pocillopora_meandrina_HIv1___xpSc0001275 48561 179890 3.7044 7.7868
Pocillopora_meandrina_HIv1___xpSc0001276 38618 36168 0.9366 3.1049
Pocillopora_meandrina_HIv1___xpSc0001280 35955 311777 8.6713 12.3223
Pocillopora_meandrina_HIv1___xpSc0001281 34238 200286 5.8498 10.1164
Pocillopora_meandrina_HIv1___xpSc0001290 28931 342155 11.8266 9.8697
Pocillopora_meandrina_HIv1___xpSc0001321 15304 78089 5.1025 8.3411
Pocillopora_meandrina_HIv1___xpSc0001331 8958 132904 14.8363 9.2089
Pocillopora_meandrina_HIv1___xpSc0001337 6786 152710 22.5037 8.6217
Pocillopora_meandrina_HIv1___xpSc0001344 5647 36727 6.5038 9.5285
Pocillopora_meandrina_HIv1___xpSc0001355 3576 57631 16.1161 9.4363

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 21:18:49
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