Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-57-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-57-TP4_R1_001.fastp-trim.fq.gz -2 POC-57-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-57-TP4 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:46:41 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-57-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 49,137,156
Mapped reads 49,137,156 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 49,137,156 / 100%
Mapped reads, first in pair 24,568,578 / 50%
Mapped reads, second in pair 24,568,578 / 50%
Mapped reads, both in pair 49,137,156 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.67
Overlapping read pairs 15,135,749 / 61.61%
Duplicated reads (estimated) 6,581,443 / 13.39%
Duplication rate 12.73%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,594,378,291 / 40.27%
Number/percentage of C's 632,323,094 / 9.82%
Number/percentage of T's 2,595,371,032 / 40.29%
Number/percentage of G's 619,227,328 / 9.61%
Number/percentage of N's 541,224 / 0.01%
GC Percentage 19.43%

Coverage

Mean 17.1606
Standard Deviation 17.8591
Mean (paired-end reads overlap ignored) 14.43

Mapping Quality

Mean Mapping Quality 22.64

Insert size

Mean 247.84
Standard Deviation 87.42
P25/Median/P75 180 / 241 / 305

Mismatches and indels

General error rate 21.16%
Mismatches 1,339,317,459
Insertions 9,452,168
Mapped reads with at least one insertion 14.54%
Deletions 7,597,559
Mapped reads with at least one deletion 12.99%
Homopolymer indels 52.26%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 403410012 18.6323 13.3664
Pocillopora_meandrina_HIv1___Sc0000001 21507942 417587503 19.4155 12.7001
Pocillopora_meandrina_HIv1___Sc0000002 19741974 374985556 18.9943 13.0519
Pocillopora_meandrina_HIv1___Sc0000003 19417450 332890515 17.1439 14.7562
Pocillopora_meandrina_HIv1___Sc0000004 14584444 236020696 16.183 19.4356
Pocillopora_meandrina_HIv1___Sc0000005 14098929 261700120 18.5617 12.8818
Pocillopora_meandrina_HIv1___Sc0000006 14068054 260722272 18.5329 13.5538
Pocillopora_meandrina_HIv1___Sc0000007 13590779 241705213 17.7845 14.434
Pocillopora_meandrina_HIv1___Sc0000008 12446599 240148400 19.2943 13.5951
Pocillopora_meandrina_HIv1___Sc0000009 11983232 112825685 9.4153 14.6435
Pocillopora_meandrina_HIv1___Sc0000010 11763137 206050508 17.5166 16.0204
Pocillopora_meandrina_HIv1___Sc0000011 10501528 219612918 20.9125 11.497
Pocillopora_meandrina_HIv1___Sc0000012 10024633 179996904 17.9555 24.4834
Pocillopora_meandrina_HIv1___Sc0000013 9946974 139427242 14.0171 13.5323
Pocillopora_meandrina_HIv1___Sc0000014 9536826 185847863 19.4874 12.6127
Pocillopora_meandrina_HIv1___Sc0000015 9393205 170474968 18.1488 13.4618
Pocillopora_meandrina_HIv1___Sc0000016 9288165 165463645 17.8145 13.615
Pocillopora_meandrina_HIv1___Sc0000017 9274345 164598942 17.7478 13.2602
Pocillopora_meandrina_HIv1___Sc0000018 8584156 165011734 19.2228 13.159
Pocillopora_meandrina_HIv1___Sc0000019 7112774 125796338 17.686 14.1042
Pocillopora_meandrina_HIv1___Sc0000020 6748058 118764607 17.5998 14.8125
Pocillopora_meandrina_HIv1___Sc0000021 6546105 124235945 18.9786 13.3305
Pocillopora_meandrina_HIv1___Sc0000022 6319256 105776644 16.7388 17.3621
Pocillopora_meandrina_HIv1___Sc0000023 5767069 91047465 15.7875 14.7206
Pocillopora_meandrina_HIv1___Sc0000024 5762297 63467548 11.0143 13.4152
Pocillopora_meandrina_HIv1___Sc0000025 5759531 86034701 14.9378 15.3465
Pocillopora_meandrina_HIv1___Sc0000026 5647578 117907966 20.8776 12.0115
Pocillopora_meandrina_HIv1___Sc0000027 5550630 92468916 16.6592 20.2786
Pocillopora_meandrina_HIv1___Sc0000028 5130920 100758572 19.6375 15.2723
Pocillopora_meandrina_HIv1___Sc0000029 4860867 76536159 15.7454 13.0907
Pocillopora_meandrina_HIv1___Sc0000030 4843735 87925861 18.1525 11.4724
Pocillopora_meandrina_HIv1___Sc0000031 4691590 85507743 18.2257 12.6207
Pocillopora_meandrina_HIv1___Sc0000032 3615800 72120454 19.9459 14.1883
Pocillopora_meandrina_HIv1___Sc0000033 3306609 45120581 13.6456 12.8938
Pocillopora_meandrina_HIv1___Sc0000034 3122802 57820960 18.5157 12.7964
Pocillopora_meandrina_HIv1___Sc0000035 3015365 44207381 14.6607 14.6649
Pocillopora_meandrina_HIv1___Sc0000036 3007169 65439474 21.7612 12.1221
Pocillopora_meandrina_HIv1___Sc0000037 2860435 57749098 20.1889 18.9172
Pocillopora_meandrina_HIv1___Sc0000038 2701138 48830456 18.0777 15.773
Pocillopora_meandrina_HIv1___Sc0000039 2599273 36848698 14.1765 13.5334
Pocillopora_meandrina_HIv1___Sc0000040 2445666 43760803 17.8932 17.4864
Pocillopora_meandrina_HIv1___Sc0000041 2159376 40212250 18.6222 12.2404
Pocillopora_meandrina_HIv1___Sc0000042 1957488 27445230 14.0206 12.2511
Pocillopora_meandrina_HIv1___Sc0000043 1845599 27002655 14.6308 12.2826
Pocillopora_meandrina_HIv1___Sc0000044 1724711 33068561 19.1734 13.7057
Pocillopora_meandrina_HIv1___Sc0000045 1153740 15232381 13.2026 12.4702
Pocillopora_meandrina_HIv1___Sc0000046 755410 9645351 12.7684 17.2652
Pocillopora_meandrina_HIv1___Sc0000047 239089 458707 1.9186 6.4891
Pocillopora_meandrina_HIv1___Sc0000048 214660 55971 0.2607 1.5983
Pocillopora_meandrina_HIv1___Sc0000049 179266 513648 2.8653 8.0668
Pocillopora_meandrina_HIv1___Sc0000050 177168 202676 1.144 3.2774
Pocillopora_meandrina_HIv1___Sc0000051 165057 825989 5.0043 8.2768
Pocillopora_meandrina_HIv1___Sc0000052 155210 101768 0.6557 7.2874
Pocillopora_meandrina_HIv1___Sc0000053 123249 312122 2.5325 6.3086
Pocillopora_meandrina_HIv1___Sc0000054 122643 1732481 14.1262 14.7656
Pocillopora_meandrina_HIv1___Sc0000055 121609 650481 5.349 11.6342
Pocillopora_meandrina_HIv1___Sc0000056 112816 79595 0.7055 7.5646
Pocillopora_meandrina_HIv1___Sc0000057 107171 433544 4.0453 9.6803
Pocillopora_meandrina_HIv1___Sc0000058 98341 95885 0.975 11.0414
Pocillopora_meandrina_HIv1___Sc0000059 83292 2394 0.0287 0.1956
Pocillopora_meandrina_HIv1___Sc0000060 79483 798 0.01 0.1112
Pocillopora_meandrina_HIv1___Sc0000061 75390 262880 3.4869 8.5782
Pocillopora_meandrina_HIv1___Sc0000062 74194 20865 0.2812 1.2902
Pocillopora_meandrina_HIv1___Sc0000063 73457 76747 1.0448 11.8968
Pocillopora_meandrina_HIv1___Sc0000064 72700 6735 0.0926 0.4834
Pocillopora_meandrina_HIv1___Sc0000065 67986 11667 0.1716 1.5651
Pocillopora_meandrina_HIv1___Sc0000066 66659 488948 7.3351 7.9733
Pocillopora_meandrina_HIv1___Sc0000067 64947 130977 2.0167 4.4729
Pocillopora_meandrina_HIv1___Sc0000068 64340 9914 0.1541 1.0679
Pocillopora_meandrina_HIv1___Sc0000069 62616 196427 3.137 8.0411
Pocillopora_meandrina_HIv1___Sc0000070 60121 175225 2.9145 13.4463
Pocillopora_meandrina_HIv1___Sc0000071 57157 59916 1.0483 2.1067
Pocillopora_meandrina_HIv1___Sc0000072 56626 15603 0.2755 2.8682
Pocillopora_meandrina_HIv1___Sc0000073 56082 7438 0.1326 0.57
Pocillopora_meandrina_HIv1___Sc0000074 55210 257 0.0047 0.0944
Pocillopora_meandrina_HIv1___Sc0000075 54685 2040 0.0373 0.3056
Pocillopora_meandrina_HIv1___Sc0000076 54587 245007 4.4884 22.6335
Pocillopora_meandrina_HIv1___Sc0000077 53379 20216 0.3787 0.9188
Pocillopora_meandrina_HIv1___Sc0000078 51564 964 0.0187 0.2822
Pocillopora_meandrina_HIv1___Sc0000079 49664 806 0.0162 0.1605
Pocillopora_meandrina_HIv1___Sc0000080 47218 113402 2.4017 6.5826
Pocillopora_meandrina_HIv1___Sc0000081 42490 13806 0.3249 1.0868
Pocillopora_meandrina_HIv1___Sc0000082 32657 566986 17.3619 37.761
Pocillopora_meandrina_HIv1___Sc0000083 27992 2119 0.0757 0.3871
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 11735132 7.3271 11.6028
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4030011 3.3647 7.5735
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5417373 6.9496 10.1041
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1586595 3.4316 5.9052
Pocillopora_meandrina_HIv1___xfSc0000004 334777 829096 2.4766 4.914
Pocillopora_meandrina_HIv1___xfSc0000006 290100 671418 2.3144 4.4655
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2906227 11.5209 17.1159
Pocillopora_meandrina_HIv1___xfSc0000012 148278 592115 3.9933 9.1079
Pocillopora_meandrina_HIv1___xfSc0000014 118081 23485 0.1989 0.904
Pocillopora_meandrina_HIv1___xfSc0000017 98555 385123 3.9077 58.68
Pocillopora_meandrina_HIv1___xfSc0000021 95778 674642 7.0438 13.8122
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1080769 11.9101 17.876
Pocillopora_meandrina_HIv1___xfSc0000029 85532 233285 2.7275 7.0221
Pocillopora_meandrina_HIv1___xfSc0000038 77395 22817 0.2948 2.0795
Pocillopora_meandrina_HIv1___xfSc0000058 69718 794174 11.3912 11.8586
Pocillopora_meandrina_HIv1___xfSc0000059 69426 567282 8.171 10.9208
Pocillopora_meandrina_HIv1___xfSc0000074 66573 402680 6.0487 7.1116
Pocillopora_meandrina_HIv1___xfSc0000081 65415 371848 5.6844 6.8204
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1063647 16.2844 13.7815
Pocillopora_meandrina_HIv1___xfSc0000092 63607 817539 12.853 14.3216
Pocillopora_meandrina_HIv1___xfSc0000094 62842 44599 0.7097 1.7715
Pocillopora_meandrina_HIv1___xfSc0000113 60556 594356 9.815 9.6818
Pocillopora_meandrina_HIv1___xfSc0000132 59032 38090 0.6452 1.6211
Pocillopora_meandrina_HIv1___xfSc0000145 58221 330553 5.6776 6.4278
Pocillopora_meandrina_HIv1___xfSc0000146 58151 165940 2.8536 7.1209
Pocillopora_meandrina_HIv1___xfSc0000168 56681 350587 6.1853 9.4131
Pocillopora_meandrina_HIv1___xfSc0000175 56271 244365 4.3426 11.6025
Pocillopora_meandrina_HIv1___xfSc0000195 55223 12134 0.2197 1.1355
Pocillopora_meandrina_HIv1___xfSc0000199 55095 304472 5.5263 11.3091
Pocillopora_meandrina_HIv1___xfSc0000205 54658 274716 5.0261 7.0021
Pocillopora_meandrina_HIv1___xfSc0000206 54623 282652 5.1746 8.1694
Pocillopora_meandrina_HIv1___xfSc0000212 54299 364479 6.7124 10.0644
Pocillopora_meandrina_HIv1___xfSc0000217 54168 528014 9.7477 20.472
Pocillopora_meandrina_HIv1___xfSc0000223 53823 390739 7.2597 8.5094
Pocillopora_meandrina_HIv1___xfSc0000228 53382 388046 7.2692 31.1992
Pocillopora_meandrina_HIv1___xfSc0000237 53049 289637 5.4598 7.9124
Pocillopora_meandrina_HIv1___xfSc0000262 52308 416220 7.9571 7.7705
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1161845 22.2303 26.4223
Pocillopora_meandrina_HIv1___xfSc0000272 52107 329734 6.328 9.5671
Pocillopora_meandrina_HIv1___xfSc0000275 51938 441924 8.5087 10.4633
Pocillopora_meandrina_HIv1___xfSc0000284 51483 563844 10.952 13.9662
Pocillopora_meandrina_HIv1___xfSc0000288 51367 355913 6.9288 15.22
Pocillopora_meandrina_HIv1___xfSc0000300 50845 6158 0.1211 0.4735
Pocillopora_meandrina_HIv1___xfSc0000301 50809 519775 10.23 12.3619
Pocillopora_meandrina_HIv1___xfSc0000343 49544 282588 5.7038 7.8996
Pocillopora_meandrina_HIv1___xfSc0000376 48519 560171 11.5454 38.5007
Pocillopora_meandrina_HIv1___xfSc0000415 47398 114027 2.4057 3.9865
Pocillopora_meandrina_HIv1___xfSc0000423 47202 53084 1.1246 3.2217
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1092084 23.1885 29.1152
Pocillopora_meandrina_HIv1___xfSc0000428 47057 741445 15.7563 26.8323
Pocillopora_meandrina_HIv1___xfSc0000436 46816 378504 8.0849 17.0516
Pocillopora_meandrina_HIv1___xfSc0000445 46561 154976 3.3285 6.8882
Pocillopora_meandrina_HIv1___xfSc0000447 46542 474119 10.1869 12.8642
Pocillopora_meandrina_HIv1___xfSc0000469 45938 514056 11.1902 10.4977
Pocillopora_meandrina_HIv1___xfSc0000477 45781 365093 7.9748 8.5546
Pocillopora_meandrina_HIv1___xfSc0000479 45736 164023 3.5863 5.7282
Pocillopora_meandrina_HIv1___xfSc0000482 45585 313148 6.8695 11.671
Pocillopora_meandrina_HIv1___xfSc0000488 45379 256223 5.6463 9.0563
Pocillopora_meandrina_HIv1___xfSc0000506 44781 144213 3.2204 5.2181
Pocillopora_meandrina_HIv1___xfSc0000527 44235 277104 6.2644 9.0002
Pocillopora_meandrina_HIv1___xfSc0000540 43935 457314 10.4089 14.3688
Pocillopora_meandrina_HIv1___xfSc0000555 43535 355056 8.1556 16.4214
Pocillopora_meandrina_HIv1___xfSc0000565 43357 621822 14.3419 12.3476
Pocillopora_meandrina_HIv1___xfSc0000566 43316 238441 5.5047 9.1817
Pocillopora_meandrina_HIv1___xfSc0000567 43305 191686 4.4264 8.8808
Pocillopora_meandrina_HIv1___xfSc0000570 43295 94382 2.18 5.6247
Pocillopora_meandrina_HIv1___xfSc0000579 43029 64350 1.4955 3.7575
Pocillopora_meandrina_HIv1___xfSc0000583 42958 358539 8.3463 8.9485
Pocillopora_meandrina_HIv1___xfSc0000596 42675 212848 4.9877 8.3175
Pocillopora_meandrina_HIv1___xfSc0000612 42423 206714 4.8727 6.6232
Pocillopora_meandrina_HIv1___xfSc0000616 42355 12372722 292.1195 893.3286
Pocillopora_meandrina_HIv1___xfSc0000621 42164 314184 7.4515 9.2528
Pocillopora_meandrina_HIv1___xfSc0000642 41754 188866 4.5233 6.5624
Pocillopora_meandrina_HIv1___xfSc0000655 41446 419106 10.1121 23.4041
Pocillopora_meandrina_HIv1___xfSc0000692 40426 57354 1.4187 4.5258
Pocillopora_meandrina_HIv1___xfSc0000699 40296 37273 0.925 2.0383
Pocillopora_meandrina_HIv1___xfSc0000704 40233 713617 17.7371 23.8114
Pocillopora_meandrina_HIv1___xfSc0000705 40197 137767 3.4273 6.7375
Pocillopora_meandrina_HIv1___xfSc0000716 39998 317605 7.9405 8.6849
Pocillopora_meandrina_HIv1___xfSc0000725 39827 145217 3.6462 11.44
Pocillopora_meandrina_HIv1___xfSc0000729 39775 14278 0.359 1.9806
Pocillopora_meandrina_HIv1___xfSc0000760 39228 3991 0.1017 0.6649
Pocillopora_meandrina_HIv1___xfSc0000763 39151 270330 6.9048 7.132
Pocillopora_meandrina_HIv1___xfSc0000765 39117 99044 2.532 5.7256
Pocillopora_meandrina_HIv1___xfSc0000788 38513 435479 11.3073 16.7431
Pocillopora_meandrina_HIv1___xfSc0000811 37888 295762 7.8062 9.7695
Pocillopora_meandrina_HIv1___xfSc0000812 37881 19593 0.5172 1.0525
Pocillopora_meandrina_HIv1___xfSc0000817 37779 479560 12.6938 9.0992
Pocillopora_meandrina_HIv1___xfSc0000824 37656 46875 1.2448 2.2971
Pocillopora_meandrina_HIv1___xfSc0000835 37434 224364 5.9936 7.5761
Pocillopora_meandrina_HIv1___xfSc0000836 37372 253341 6.7789 10.4946
Pocillopora_meandrina_HIv1___xfSc0000837 37368 101098 2.7055 5.9638
Pocillopora_meandrina_HIv1___xfSc0000840 37283 232605 6.2389 16.0896
Pocillopora_meandrina_HIv1___xfSc0000857 37006 145114 3.9214 5.5821
Pocillopora_meandrina_HIv1___xfSc0000859 36995 50174 1.3562 2.6595
Pocillopora_meandrina_HIv1___xfSc0000866 36925 57156 1.5479 3.0394
Pocillopora_meandrina_HIv1___xfSc0000868 36831 107768 2.926 8.5332
Pocillopora_meandrina_HIv1___xfSc0000875 36611 51494 1.4065 3.694
Pocillopora_meandrina_HIv1___xfSc0000885 36416 200712 5.5116 6.9848
Pocillopora_meandrina_HIv1___xfSc0000886 36355 204144 5.6153 8.9108
Pocillopora_meandrina_HIv1___xfSc0000890 36339 210087 5.7813 11.9266
Pocillopora_meandrina_HIv1___xfSc0000892 36267 111332 3.0698 13.0645
Pocillopora_meandrina_HIv1___xfSc0000943 35168 6021 0.1712 0.9187
Pocillopora_meandrina_HIv1___xfSc0000948 35100 226630 6.4567 8.7
Pocillopora_meandrina_HIv1___xfSc0000952 34934 215236 6.1612 8.2531
Pocillopora_meandrina_HIv1___xfSc0000953 34905 176322 5.0515 6.2474
Pocillopora_meandrina_HIv1___xfSc0000957 34773 276395 7.9486 9.4005
Pocillopora_meandrina_HIv1___xfSc0000968 34345 12676 0.3691 1.595
Pocillopora_meandrina_HIv1___xfSc0000974 34140 311839 9.1341 10.4732
Pocillopora_meandrina_HIv1___xfSc0000975 33988 348432 10.2516 9.6642
Pocillopora_meandrina_HIv1___xfSc0000995 33324 86196 2.5866 5.8487
Pocillopora_meandrina_HIv1___xfSc0001011 32918 137351 4.1725 7.8006
Pocillopora_meandrina_HIv1___xfSc0001122 29140 253065 8.6845 11.1274
Pocillopora_meandrina_HIv1___xfSc0001170 27381 15617 0.5704 1.7391
Pocillopora_meandrina_HIv1___xfSc0001179 27200 101304 3.7244 5.9115
Pocillopora_meandrina_HIv1___xfSc0001231 22938 17520 0.7638 1.5259
Pocillopora_meandrina_HIv1___xfSc0001237 22715 103740 4.567 11.4971
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2053260 5.0292 10.0748
Pocillopora_meandrina_HIv1___xpSc0001275 48561 194355 4.0023 8.5476
Pocillopora_meandrina_HIv1___xpSc0001276 38618 57226 1.4818 4.2443
Pocillopora_meandrina_HIv1___xpSc0001280 35955 179490 4.9921 7.7485
Pocillopora_meandrina_HIv1___xpSc0001281 34238 193492 5.6514 8.3665
Pocillopora_meandrina_HIv1___xpSc0001290 28931 286698 9.9097 10.0908
Pocillopora_meandrina_HIv1___xpSc0001321 15304 36735 2.4004 4.9968
Pocillopora_meandrina_HIv1___xpSc0001331 8958 186873 20.861 9.7265
Pocillopora_meandrina_HIv1___xpSc0001337 6786 32430 4.779 9.5253
Pocillopora_meandrina_HIv1___xpSc0001344 5647 73087 12.9426 16.4922
Pocillopora_meandrina_HIv1___xpSc0001355 3576 35831 10.0199 8.4333

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 20:46:44
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