Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-57-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-57-TP1_R1_001.fastp-trim.fq.gz -2 POC-57-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-57-TP1 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:01:17 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-57-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 42,137,180
Mapped reads 42,137,180 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 42,137,180 / 100%
Mapped reads, first in pair 21,068,590 / 50%
Mapped reads, second in pair 21,068,590 / 50%
Mapped reads, both in pair 42,137,180 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.12
Overlapping read pairs 12,668,272 / 60.13%
Duplicated reads (estimated) 4,679,681 / 11.11%
Duplication rate 10.7%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,235,178,510 / 40.32%
Number/percentage of C's 540,454,072 / 9.75%
Number/percentage of T's 2,237,325,576 / 40.36%
Number/percentage of G's 529,584,773 / 9.55%
Number/percentage of N's 463,199 / 0.01%
GC Percentage 19.3%

Coverage

Mean 14.7665
Standard Deviation 13.3722
Mean (paired-end reads overlap ignored) 12.49

Mapping Quality

Mean Mapping Quality 22.69

Insert size

Mean 251.53
Standard Deviation 87.93
P25/Median/P75 183 / 245 / 309

Mismatches and indels

General error rate 21.15%
Mismatches 1,151,562,805
Insertions 8,165,754
Mapped reads with at least one insertion 14.65%
Deletions 6,591,243
Mapped reads with at least one deletion 13.13%
Homopolymer indels 52.28%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 344772873 15.924 11.2808
Pocillopora_meandrina_HIv1___Sc0000001 21507942 358255327 16.6569 11.1287
Pocillopora_meandrina_HIv1___Sc0000002 19741974 321637378 16.2921 11.0827
Pocillopora_meandrina_HIv1___Sc0000003 19417450 281327879 14.4884 12.1414
Pocillopora_meandrina_HIv1___Sc0000004 14584444 210036715 14.4014 17.6151
Pocillopora_meandrina_HIv1___Sc0000005 14098929 224461020 15.9204 10.788
Pocillopora_meandrina_HIv1___Sc0000006 14068054 222207224 15.7952 12.0403
Pocillopora_meandrina_HIv1___Sc0000007 13590779 210150551 15.4627 12.4852
Pocillopora_meandrina_HIv1___Sc0000008 12446599 210152178 16.8843 11.7772
Pocillopora_meandrina_HIv1___Sc0000009 11983232 121019646 10.0991 14.5707
Pocillopora_meandrina_HIv1___Sc0000010 11763137 171006518 14.5375 12.8459
Pocillopora_meandrina_HIv1___Sc0000011 10501528 184203052 17.5406 9.7601
Pocillopora_meandrina_HIv1___Sc0000012 10024633 155546069 15.5164 15.8998
Pocillopora_meandrina_HIv1___Sc0000013 9946974 120922844 12.1567 11.7997
Pocillopora_meandrina_HIv1___Sc0000014 9536826 158918259 16.6636 11.0955
Pocillopora_meandrina_HIv1___Sc0000015 9393205 140180894 14.9236 10.9358
Pocillopora_meandrina_HIv1___Sc0000016 9288165 139088205 14.9748 11.639
Pocillopora_meandrina_HIv1___Sc0000017 9274345 138399923 14.9229 11.4807
Pocillopora_meandrina_HIv1___Sc0000018 8584156 138188011 16.098 11.0505
Pocillopora_meandrina_HIv1___Sc0000019 7112774 108704047 15.2829 11.9984
Pocillopora_meandrina_HIv1___Sc0000020 6748058 113085222 16.7582 17.4556
Pocillopora_meandrina_HIv1___Sc0000021 6546105 107913872 16.4852 11.5221
Pocillopora_meandrina_HIv1___Sc0000022 6319256 90433634 14.3108 13.9753
Pocillopora_meandrina_HIv1___Sc0000023 5767069 73632918 12.7678 11.7178
Pocillopora_meandrina_HIv1___Sc0000024 5762297 57970933 10.0604 11.5837
Pocillopora_meandrina_HIv1___Sc0000025 5759531 74050559 12.857 12.9785
Pocillopora_meandrina_HIv1___Sc0000026 5647578 102660685 18.1778 11.2328
Pocillopora_meandrina_HIv1___Sc0000027 5550630 77623291 13.9846 15.4481
Pocillopora_meandrina_HIv1___Sc0000028 5130920 90816438 17.6998 14.015
Pocillopora_meandrina_HIv1___Sc0000029 4860867 65865718 13.5502 11.2444
Pocillopora_meandrina_HIv1___Sc0000030 4843735 77274081 15.9534 10.6605
Pocillopora_meandrina_HIv1___Sc0000031 4691590 71217771 15.1799 10.6884
Pocillopora_meandrina_HIv1___Sc0000032 3615800 62180625 17.1969 12.4929
Pocillopora_meandrina_HIv1___Sc0000033 3306609 37149997 11.2351 11.5097
Pocillopora_meandrina_HIv1___Sc0000034 3122802 49904749 15.9808 11.5182
Pocillopora_meandrina_HIv1___Sc0000035 3015365 39974119 13.2568 13.4597
Pocillopora_meandrina_HIv1___Sc0000036 3007169 52790157 17.5548 10.0912
Pocillopora_meandrina_HIv1___Sc0000037 2860435 45786957 16.007 13.2033
Pocillopora_meandrina_HIv1___Sc0000038 2701138 40433563 14.9691 12.5175
Pocillopora_meandrina_HIv1___Sc0000039 2599273 31854266 12.2551 12.2001
Pocillopora_meandrina_HIv1___Sc0000040 2445666 34731167 14.2011 13.1832
Pocillopora_meandrina_HIv1___Sc0000041 2159376 35034848 16.2245 10.723
Pocillopora_meandrina_HIv1___Sc0000042 1957488 25271933 12.9104 10.916
Pocillopora_meandrina_HIv1___Sc0000043 1845599 22983070 12.4529 10.716
Pocillopora_meandrina_HIv1___Sc0000044 1724711 26553244 15.3958 11.4411
Pocillopora_meandrina_HIv1___Sc0000045 1153740 15305221 13.2657 12.3272
Pocillopora_meandrina_HIv1___Sc0000046 755410 7553314 9.999 12.3119
Pocillopora_meandrina_HIv1___Sc0000047 239089 308651 1.2909 3.8322
Pocillopora_meandrina_HIv1___Sc0000048 214660 45675 0.2128 1.1549
Pocillopora_meandrina_HIv1___Sc0000049 179266 226114 1.2613 5.7537
Pocillopora_meandrina_HIv1___Sc0000050 177168 187457 1.0581 3.0336
Pocillopora_meandrina_HIv1___Sc0000051 165057 697547 4.2261 6.9145
Pocillopora_meandrina_HIv1___Sc0000052 155210 74001 0.4768 5.7668
Pocillopora_meandrina_HIv1___Sc0000053 123249 203504 1.6512 3.9656
Pocillopora_meandrina_HIv1___Sc0000054 122643 1596027 13.0136 13.6105
Pocillopora_meandrina_HIv1___Sc0000055 121609 367719 3.0238 6.3874
Pocillopora_meandrina_HIv1___Sc0000056 112816 49644 0.44 4.7218
Pocillopora_meandrina_HIv1___Sc0000057 107171 466475 4.3526 9.0837
Pocillopora_meandrina_HIv1___Sc0000058 98341 72824 0.7405 8.7193
Pocillopora_meandrina_HIv1___Sc0000059 83292 1081 0.013 0.1377
Pocillopora_meandrina_HIv1___Sc0000060 79483 522 0.0066 0.1
Pocillopora_meandrina_HIv1___Sc0000061 75390 142264 1.887 4.0148
Pocillopora_meandrina_HIv1___Sc0000062 74194 12074 0.1627 0.809
Pocillopora_meandrina_HIv1___Sc0000063 73457 13835 0.1883 1.5218
Pocillopora_meandrina_HIv1___Sc0000064 72700 2993 0.0412 0.2596
Pocillopora_meandrina_HIv1___Sc0000065 67986 2580 0.0379 0.2763
Pocillopora_meandrina_HIv1___Sc0000066 66659 452483 6.788 7.3384
Pocillopora_meandrina_HIv1___Sc0000067 64947 105112 1.6184 3.4276
Pocillopora_meandrina_HIv1___Sc0000068 64340 8723 0.1356 1.0209
Pocillopora_meandrina_HIv1___Sc0000069 62616 168138 2.6852 6.9555
Pocillopora_meandrina_HIv1___Sc0000070 60121 230390 3.8321 21.4176
Pocillopora_meandrina_HIv1___Sc0000071 57157 52655 0.9212 1.833
Pocillopora_meandrina_HIv1___Sc0000072 56626 9372 0.1655 1.7199
Pocillopora_meandrina_HIv1___Sc0000073 56082 9268 0.1653 0.7319
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 1052 0.0192 0.1862
Pocillopora_meandrina_HIv1___Sc0000076 54587 195010 3.5725 17.8693
Pocillopora_meandrina_HIv1___Sc0000077 53379 20722 0.3882 0.9553
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1798 0.0362 0.2828
Pocillopora_meandrina_HIv1___Sc0000080 47218 93292 1.9758 5.2786
Pocillopora_meandrina_HIv1___Sc0000081 42490 6154 0.1448 0.7221
Pocillopora_meandrina_HIv1___Sc0000082 32657 511191 15.6533 34.3069
Pocillopora_meandrina_HIv1___Sc0000083 27992 2969 0.1061 0.4722
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 7270695 4.5396 8.4112
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 6039840 5.0428 9.53
Pocillopora_meandrina_HIv1___xfSc0000002 779520 6736351 8.6417 11.5314
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2097489 4.5366 8.3304
Pocillopora_meandrina_HIv1___xfSc0000004 334777 988721 2.9534 5.3843
Pocillopora_meandrina_HIv1___xfSc0000006 290100 660420 2.2765 4.4803
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2015590 7.9902 10.3422
Pocillopora_meandrina_HIv1___xfSc0000012 148278 494271 3.3334 7.1725
Pocillopora_meandrina_HIv1___xfSc0000014 118081 19342 0.1638 0.7676
Pocillopora_meandrina_HIv1___xfSc0000017 98555 400313 4.0618 62.4219
Pocillopora_meandrina_HIv1___xfSc0000021 95778 606484 6.3322 11.4987
Pocillopora_meandrina_HIv1___xfSc0000024 90744 528577 5.8249 9.2188
Pocillopora_meandrina_HIv1___xfSc0000029 85532 183095 2.1407 5.865
Pocillopora_meandrina_HIv1___xfSc0000038 77395 31712 0.4097 3.6259
Pocillopora_meandrina_HIv1___xfSc0000058 69718 428063 6.1399 9.1619
Pocillopora_meandrina_HIv1___xfSc0000059 69426 403464 5.8114 8.4916
Pocillopora_meandrina_HIv1___xfSc0000074 66573 248451 3.732 6.2517
Pocillopora_meandrina_HIv1___xfSc0000081 65415 205177 3.1365 5.2144
Pocillopora_meandrina_HIv1___xfSc0000083 65317 709636 10.8645 10.1354
Pocillopora_meandrina_HIv1___xfSc0000092 63607 483628 7.6034 9.094
Pocillopora_meandrina_HIv1___xfSc0000094 62842 86333 1.3738 3.4272
Pocillopora_meandrina_HIv1___xfSc0000113 60556 960215 15.8566 18.9179
Pocillopora_meandrina_HIv1___xfSc0000132 59032 34655 0.5871 1.6134
Pocillopora_meandrina_HIv1___xfSc0000145 58221 540252 9.2793 8.3549
Pocillopora_meandrina_HIv1___xfSc0000146 58151 129668 2.2298 5.5633
Pocillopora_meandrina_HIv1___xfSc0000168 56681 292164 5.1545 7.7615
Pocillopora_meandrina_HIv1___xfSc0000175 56271 246513 4.3808 11.0222
Pocillopora_meandrina_HIv1___xfSc0000195 55223 5272 0.0955 0.6906
Pocillopora_meandrina_HIv1___xfSc0000199 55095 754336 13.6916 21.5818
Pocillopora_meandrina_HIv1___xfSc0000205 54658 304681 5.5743 10.3108
Pocillopora_meandrina_HIv1___xfSc0000206 54623 204568 3.7451 5.9542
Pocillopora_meandrina_HIv1___xfSc0000212 54299 317272 5.8431 8.8138
Pocillopora_meandrina_HIv1___xfSc0000217 54168 301291 5.5622 13.8091
Pocillopora_meandrina_HIv1___xfSc0000223 53823 365199 6.7852 7.9571
Pocillopora_meandrina_HIv1___xfSc0000228 53382 454775 8.5193 29.6288
Pocillopora_meandrina_HIv1___xfSc0000237 53049 253129 4.7716 7.1325
Pocillopora_meandrina_HIv1___xfSc0000262 52308 175487 3.3549 5.4269
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1212406 23.1977 21.4332
Pocillopora_meandrina_HIv1___xfSc0000272 52107 284934 5.4682 8.2148
Pocillopora_meandrina_HIv1___xfSc0000275 51938 160741 3.0949 6.3548
Pocillopora_meandrina_HIv1___xfSc0000284 51483 396065 7.6931 9.4796
Pocillopora_meandrina_HIv1___xfSc0000288 51367 762314 14.8405 16.6975
Pocillopora_meandrina_HIv1___xfSc0000300 50845 10238 0.2014 0.6993
Pocillopora_meandrina_HIv1___xfSc0000301 50809 421528 8.2963 8.7538
Pocillopora_meandrina_HIv1___xfSc0000343 49544 162953 3.2891 6.6754
Pocillopora_meandrina_HIv1___xfSc0000376 48519 340403 7.0159 19.9902
Pocillopora_meandrina_HIv1___xfSc0000415 47398 386516 8.1547 9.8296
Pocillopora_meandrina_HIv1___xfSc0000423 47202 42928 0.9095 2.4404
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1355544 28.7826 31.6868
Pocillopora_meandrina_HIv1___xfSc0000428 47057 410353 8.7203 18.5947
Pocillopora_meandrina_HIv1___xfSc0000436 46816 393731 8.4102 18.4766
Pocillopora_meandrina_HIv1___xfSc0000445 46561 69356 1.4896 3.2783
Pocillopora_meandrina_HIv1___xfSc0000447 46542 250698 5.3865 6.9519
Pocillopora_meandrina_HIv1___xfSc0000469 45938 375255 8.1687 8.0676
Pocillopora_meandrina_HIv1___xfSc0000477 45781 470001 10.2663 13.2491
Pocillopora_meandrina_HIv1___xfSc0000479 45736 163489 3.5746 5.7793
Pocillopora_meandrina_HIv1___xfSc0000482 45585 756495 16.5953 25.7333
Pocillopora_meandrina_HIv1___xfSc0000488 45379 274487 6.0488 9.4204
Pocillopora_meandrina_HIv1___xfSc0000506 44781 195746 4.3712 6.1322
Pocillopora_meandrina_HIv1___xfSc0000527 44235 270337 6.1114 9.3646
Pocillopora_meandrina_HIv1___xfSc0000540 43935 288180 6.5592 8.0918
Pocillopora_meandrina_HIv1___xfSc0000555 43535 210070 4.8253 8.2852
Pocillopora_meandrina_HIv1___xfSc0000565 43357 325244 7.5015 7.818
Pocillopora_meandrina_HIv1___xfSc0000566 43316 204564 4.7226 6.8179
Pocillopora_meandrina_HIv1___xfSc0000567 43305 171746 3.966 8.0816
Pocillopora_meandrina_HIv1___xfSc0000570 43295 84510 1.952 5.2786
Pocillopora_meandrina_HIv1___xfSc0000579 43029 54144 1.2583 3.2318
Pocillopora_meandrina_HIv1___xfSc0000583 42958 305021 7.1004 7.9022
Pocillopora_meandrina_HIv1___xfSc0000596 42675 209915 4.9189 8.7242
Pocillopora_meandrina_HIv1___xfSc0000612 42423 115512 2.7229 4.4567
Pocillopora_meandrina_HIv1___xfSc0000616 42355 5677375 134.0426 395.9169
Pocillopora_meandrina_HIv1___xfSc0000621 42164 396218 9.3971 10.6374
Pocillopora_meandrina_HIv1___xfSc0000642 41754 140786 3.3718 6.527
Pocillopora_meandrina_HIv1___xfSc0000655 41446 237775 5.737 11.8714
Pocillopora_meandrina_HIv1___xfSc0000692 40426 349171 8.6373 10.1499
Pocillopora_meandrina_HIv1___xfSc0000699 40296 29730 0.7378 1.7849
Pocillopora_meandrina_HIv1___xfSc0000704 40233 487705 12.122 15.7299
Pocillopora_meandrina_HIv1___xfSc0000705 40197 120841 3.0062 5.9536
Pocillopora_meandrina_HIv1___xfSc0000716 39998 157972 3.9495 6.1675
Pocillopora_meandrina_HIv1___xfSc0000725 39827 91740 2.3035 7.5103
Pocillopora_meandrina_HIv1___xfSc0000729 39775 27459 0.6904 5.4371
Pocillopora_meandrina_HIv1___xfSc0000760 39228 4920 0.1254 0.7662
Pocillopora_meandrina_HIv1___xfSc0000763 39151 248351 6.3434 6.3243
Pocillopora_meandrina_HIv1___xfSc0000765 39117 93187 2.3823 5.4636
Pocillopora_meandrina_HIv1___xfSc0000788 38513 274454 7.1263 9.0673
Pocillopora_meandrina_HIv1___xfSc0000811 37888 485855 12.8235 11.7322
Pocillopora_meandrina_HIv1___xfSc0000812 37881 24403 0.6442 1.3807
Pocillopora_meandrina_HIv1___xfSc0000817 37779 377594 9.9948 9.3964
Pocillopora_meandrina_HIv1___xfSc0000824 37656 234775 6.2347 9.7191
Pocillopora_meandrina_HIv1___xfSc0000835 37434 126328 3.3747 5.836
Pocillopora_meandrina_HIv1___xfSc0000836 37372 205679 5.5036 10.4315
Pocillopora_meandrina_HIv1___xfSc0000837 37368 309466 8.2816 7.1691
Pocillopora_meandrina_HIv1___xfSc0000840 37283 307038 8.2353 16.2088
Pocillopora_meandrina_HIv1___xfSc0000857 37006 182019 4.9186 6.7794
Pocillopora_meandrina_HIv1___xfSc0000859 36995 38716 1.0465 2.0314
Pocillopora_meandrina_HIv1___xfSc0000866 36925 61803 1.6737 3.2634
Pocillopora_meandrina_HIv1___xfSc0000868 36831 108714 2.9517 6.1032
Pocillopora_meandrina_HIv1___xfSc0000875 36611 27104 0.7403 2.1129
Pocillopora_meandrina_HIv1___xfSc0000885 36416 309694 8.5043 12.9969
Pocillopora_meandrina_HIv1___xfSc0000886 36355 156405 4.3022 9.5457
Pocillopora_meandrina_HIv1___xfSc0000890 36339 199002 5.4763 7.2934
Pocillopora_meandrina_HIv1___xfSc0000892 36267 148607 4.0976 19.5664
Pocillopora_meandrina_HIv1___xfSc0000943 35168 9134 0.2597 1.0089
Pocillopora_meandrina_HIv1___xfSc0000948 35100 196935 5.6107 7.9491
Pocillopora_meandrina_HIv1___xfSc0000952 34934 94714 2.7112 6.2671
Pocillopora_meandrina_HIv1___xfSc0000953 34905 158364 4.537 6.1349
Pocillopora_meandrina_HIv1___xfSc0000957 34773 232047 6.6732 11.7876
Pocillopora_meandrina_HIv1___xfSc0000968 34345 11499 0.3348 1.2278
Pocillopora_meandrina_HIv1___xfSc0000974 34140 227611 6.667 7.1078
Pocillopora_meandrina_HIv1___xfSc0000975 33988 309233 9.0983 9.2302
Pocillopora_meandrina_HIv1___xfSc0000995 33324 104226 3.1277 7.736
Pocillopora_meandrina_HIv1___xfSc0001011 32918 269358 8.1827 17.5013
Pocillopora_meandrina_HIv1___xfSc0001122 29140 439865 15.0949 11.8852
Pocillopora_meandrina_HIv1___xfSc0001170 27381 21087 0.7701 2.2781
Pocillopora_meandrina_HIv1___xfSc0001179 27200 85495 3.1432 5.6705
Pocillopora_meandrina_HIv1___xfSc0001231 22938 17467 0.7615 1.601
Pocillopora_meandrina_HIv1___xfSc0001237 22715 71084 3.1294 7.9231
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2829676 6.9309 11.4246
Pocillopora_meandrina_HIv1___xpSc0001275 48561 155787 3.2081 6.8281
Pocillopora_meandrina_HIv1___xpSc0001276 38618 32611 0.8445 2.5512
Pocillopora_meandrina_HIv1___xpSc0001280 35955 260521 7.2458 9.6817
Pocillopora_meandrina_HIv1___xpSc0001281 34238 188254 5.4984 9.205
Pocillopora_meandrina_HIv1___xpSc0001290 28931 312548 10.8032 9.5541
Pocillopora_meandrina_HIv1___xpSc0001321 15304 70075 4.5789 7.6226
Pocillopora_meandrina_HIv1___xpSc0001331 8958 108584 12.1215 7.3737
Pocillopora_meandrina_HIv1___xpSc0001337 6786 142457 20.9928 7.6368
Pocillopora_meandrina_HIv1___xpSc0001344 5647 28955 5.1275 6.3433
Pocillopora_meandrina_HIv1___xpSc0001355 3576 55303 15.465 10.183

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 21:01:18
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