Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-52-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-52-TP3_R1_001.fastp-trim.fq.gz -2 POC-52-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-52-TP3 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 02:03:31 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-52-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 60,471,868
Mapped reads 60,471,868 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 60,471,868 / 100%
Mapped reads, first in pair 30,235,934 / 50%
Mapped reads, second in pair 30,235,934 / 50%
Mapped reads, both in pair 60,471,868 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.9
Overlapping read pairs 20,331,909 / 67.24%
Duplicated reads (estimated) 9,297,526 / 15.37%
Duplication rate 14.71%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 3,200,501,390 / 40.3%
Number/percentage of C's 776,154,539 / 9.77%
Number/percentage of T's 3,202,319,964 / 40.33%
Number/percentage of G's 761,169,574 / 9.59%
Number/percentage of N's 660,759 / 0.01%
GC Percentage 19.36%

Coverage

Mean 21.1546
Standard Deviation 18.4674
Mean (paired-end reads overlap ignored) 17.44

Mapping Quality

Mean Mapping Quality 22.51

Insert size

Mean 238.33
Standard Deviation 82.17
P25/Median/P75 175 / 230 / 289

Mismatches and indels

General error rate 21.08%
Mismatches 1,644,196,952
Insertions 11,876,109
Mapped reads with at least one insertion 14.76%
Deletions 9,489,951
Mapped reads with at least one deletion 13.16%
Homopolymer indels 52.29%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 483688490 22.3401 15.9122
Pocillopora_meandrina_HIv1___Sc0000001 21507942 514146714 23.905 16.0152
Pocillopora_meandrina_HIv1___Sc0000002 19741974 464914787 23.5496 15.714
Pocillopora_meandrina_HIv1___Sc0000003 19417450 406455604 20.9325 18.4854
Pocillopora_meandrina_HIv1___Sc0000004 14584444 301552928 20.6763 27.5716
Pocillopora_meandrina_HIv1___Sc0000005 14098929 319106254 22.6334 14.7523
Pocillopora_meandrina_HIv1___Sc0000006 14068054 315810508 22.4488 17.9979
Pocillopora_meandrina_HIv1___Sc0000007 13590779 299847040 22.0625 17.0608
Pocillopora_meandrina_HIv1___Sc0000008 12446599 300687606 24.1582 16.5759
Pocillopora_meandrina_HIv1___Sc0000009 11983232 192450740 16.06 25.5319
Pocillopora_meandrina_HIv1___Sc0000010 11763137 247522171 21.0422 18.9424
Pocillopora_meandrina_HIv1___Sc0000011 10501528 273838787 26.0761 15.1905
Pocillopora_meandrina_HIv1___Sc0000012 10024633 220713823 22.0171 18.6811
Pocillopora_meandrina_HIv1___Sc0000013 9946974 167273070 16.8165 16.5434
Pocillopora_meandrina_HIv1___Sc0000014 9536826 231953964 24.3219 15.7244
Pocillopora_meandrina_HIv1___Sc0000015 9393205 202379287 21.5453 15.5269
Pocillopora_meandrina_HIv1___Sc0000016 9288165 194330700 20.9224 15.7142
Pocillopora_meandrina_HIv1___Sc0000017 9274345 198627754 21.4169 15.7353
Pocillopora_meandrina_HIv1___Sc0000018 8584156 194756014 22.6878 15.1671
Pocillopora_meandrina_HIv1___Sc0000019 7112774 157319729 22.1179 17.3958
Pocillopora_meandrina_HIv1___Sc0000020 6748058 155649079 23.0658 20.8778
Pocillopora_meandrina_HIv1___Sc0000021 6546105 154197947 23.5557 15.5226
Pocillopora_meandrina_HIv1___Sc0000022 6319256 126607992 20.0353 20.0386
Pocillopora_meandrina_HIv1___Sc0000023 5767069 107151522 18.5799 16.6703
Pocillopora_meandrina_HIv1___Sc0000024 5762297 84516404 14.6671 17.541
Pocillopora_meandrina_HIv1___Sc0000025 5759531 113663864 19.7349 19.0389
Pocillopora_meandrina_HIv1___Sc0000026 5647578 144212832 25.5353 15.2743
Pocillopora_meandrina_HIv1___Sc0000027 5550630 110914456 19.9823 22.9468
Pocillopora_meandrina_HIv1___Sc0000028 5130920 122617624 23.8978 17.8854
Pocillopora_meandrina_HIv1___Sc0000029 4860867 88096308 18.1236 16.9194
Pocillopora_meandrina_HIv1___Sc0000030 4843735 115270554 23.7979 15.8699
Pocillopora_meandrina_HIv1___Sc0000031 4691590 104581276 22.2912 15.2571
Pocillopora_meandrina_HIv1___Sc0000032 3615800 88038608 24.3483 17.312
Pocillopora_meandrina_HIv1___Sc0000033 3306609 57931421 17.5199 17.2558
Pocillopora_meandrina_HIv1___Sc0000034 3122802 72205094 23.1219 15.9117
Pocillopora_meandrina_HIv1___Sc0000035 3015365 51059705 16.9332 19.0569
Pocillopora_meandrina_HIv1___Sc0000036 3007169 82839174 27.5472 15.5432
Pocillopora_meandrina_HIv1___Sc0000037 2860435 61144354 21.3759 17.8804
Pocillopora_meandrina_HIv1___Sc0000038 2701138 53730767 19.8919 18.9188
Pocillopora_meandrina_HIv1___Sc0000039 2599273 45513720 17.5102 22.9542
Pocillopora_meandrina_HIv1___Sc0000040 2445666 47480449 19.4141 18.3578
Pocillopora_meandrina_HIv1___Sc0000041 2159376 50897587 23.5705 16.4264
Pocillopora_meandrina_HIv1___Sc0000042 1957488 40359990 20.6183 16.3855
Pocillopora_meandrina_HIv1___Sc0000043 1845599 34036886 18.4422 14.9655
Pocillopora_meandrina_HIv1___Sc0000044 1724711 39871998 23.1181 16.288
Pocillopora_meandrina_HIv1___Sc0000045 1153740 20801400 18.0295 16.444
Pocillopora_meandrina_HIv1___Sc0000046 755410 11254174 14.8981 19.3405
Pocillopora_meandrina_HIv1___Sc0000047 239089 196224 0.8207 2.9414
Pocillopora_meandrina_HIv1___Sc0000048 214660 54732 0.255 1.6171
Pocillopora_meandrina_HIv1___Sc0000049 179266 1021530 5.6984 12.4071
Pocillopora_meandrina_HIv1___Sc0000050 177168 259941 1.4672 3.6396
Pocillopora_meandrina_HIv1___Sc0000051 165057 1164658 7.0561 11.7134
Pocillopora_meandrina_HIv1___Sc0000052 155210 35157 0.2265 2.3991
Pocillopora_meandrina_HIv1___Sc0000053 123249 314103 2.5485 8.2518
Pocillopora_meandrina_HIv1___Sc0000054 122643 2332319 19.0171 27.1237
Pocillopora_meandrina_HIv1___Sc0000055 121609 723774 5.9516 13.0903
Pocillopora_meandrina_HIv1___Sc0000056 112816 80956 0.7176 6.4779
Pocillopora_meandrina_HIv1___Sc0000057 107171 642373 5.9939 13.7662
Pocillopora_meandrina_HIv1___Sc0000058 98341 43230 0.4396 4.5649
Pocillopora_meandrina_HIv1___Sc0000059 83292 3746 0.045 0.2885
Pocillopora_meandrina_HIv1___Sc0000060 79483 521 0.0066 0.0889
Pocillopora_meandrina_HIv1___Sc0000061 75390 518423 6.8765 15.8105
Pocillopora_meandrina_HIv1___Sc0000062 74194 19640 0.2647 1.2265
Pocillopora_meandrina_HIv1___Sc0000063 73457 63554 0.8652 9.0245
Pocillopora_meandrina_HIv1___Sc0000064 72700 7816 0.1075 0.5632
Pocillopora_meandrina_HIv1___Sc0000065 67986 4730 0.0696 0.4581
Pocillopora_meandrina_HIv1___Sc0000066 66659 622636 9.3406 9.7838
Pocillopora_meandrina_HIv1___Sc0000067 64947 222918 3.4323 6.847
Pocillopora_meandrina_HIv1___Sc0000068 64340 10200 0.1585 1.0109
Pocillopora_meandrina_HIv1___Sc0000069 62616 229875 3.6712 9.6783
Pocillopora_meandrina_HIv1___Sc0000070 60121 52778 0.8779 3.7608
Pocillopora_meandrina_HIv1___Sc0000071 57157 61580 1.0774 2.4581
Pocillopora_meandrina_HIv1___Sc0000072 56626 15994 0.2824 3.5495
Pocillopora_meandrina_HIv1___Sc0000073 56082 22755 0.4057 1.6715
Pocillopora_meandrina_HIv1___Sc0000074 55210 533 0.0097 0.1566
Pocillopora_meandrina_HIv1___Sc0000075 54685 741 0.0136 0.1371
Pocillopora_meandrina_HIv1___Sc0000076 54587 241554 4.4251 21.8133
Pocillopora_meandrina_HIv1___Sc0000077 53379 22116 0.4143 1.1628
Pocillopora_meandrina_HIv1___Sc0000078 51564 533 0.0103 0.1016
Pocillopora_meandrina_HIv1___Sc0000079 49664 1063 0.0214 0.1691
Pocillopora_meandrina_HIv1___Sc0000080 47218 126164 2.6719 7.1937
Pocillopora_meandrina_HIv1___Sc0000081 42490 18909 0.445 1.4213
Pocillopora_meandrina_HIv1___Sc0000082 32657 876064 26.8262 60.6298
Pocillopora_meandrina_HIv1___Sc0000083 27992 3803 0.1359 0.8723
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 16536693 10.325 17.6201
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5827753 4.8657 9.9312
Pocillopora_meandrina_HIv1___xfSc0000002 779520 8233113 10.5618 13.6634
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2248503 4.8632 10.2356
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1020762 3.0491 6.1374
Pocillopora_meandrina_HIv1___xfSc0000006 290100 811502 2.7973 5.5519
Pocillopora_meandrina_HIv1___xfSc0000007 252258 908103 3.5999 6.5458
Pocillopora_meandrina_HIv1___xfSc0000012 148278 668437 4.508 8.9623
Pocillopora_meandrina_HIv1___xfSc0000014 118081 33778 0.2861 1.1093
Pocillopora_meandrina_HIv1___xfSc0000017 98555 754008 7.6506 117.9965
Pocillopora_meandrina_HIv1___xfSc0000021 95778 842204 8.7933 16.3182
Pocillopora_meandrina_HIv1___xfSc0000024 90744 798319 8.7975 13.2548
Pocillopora_meandrina_HIv1___xfSc0000029 85532 116742 1.3649 5.1975
Pocillopora_meandrina_HIv1___xfSc0000038 77395 118566 1.532 16.6037
Pocillopora_meandrina_HIv1___xfSc0000058 69718 801109 11.4907 17.2057
Pocillopora_meandrina_HIv1___xfSc0000059 69426 391391 5.6375 12.2144
Pocillopora_meandrina_HIv1___xfSc0000074 66573 693515 10.4174 12.5517
Pocillopora_meandrina_HIv1___xfSc0000081 65415 692165 10.5811 12.6638
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1186669 18.1678 19.4556
Pocillopora_meandrina_HIv1___xfSc0000092 63607 736182 11.5739 12.9982
Pocillopora_meandrina_HIv1___xfSc0000094 62842 80680 1.2839 3.6668
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1129650 18.6546 21.1977
Pocillopora_meandrina_HIv1___xfSc0000132 59032 62860 1.0648 3.0598
Pocillopora_meandrina_HIv1___xfSc0000145 58221 371068 6.3734 7.6258
Pocillopora_meandrina_HIv1___xfSc0000146 58151 174612 3.0027 6.813
Pocillopora_meandrina_HIv1___xfSc0000168 56681 449496 7.9303 11.9669
Pocillopora_meandrina_HIv1___xfSc0000175 56271 337042 5.9896 17.672
Pocillopora_meandrina_HIv1___xfSc0000195 55223 19804 0.3586 3.1707
Pocillopora_meandrina_HIv1___xfSc0000199 55095 601943 10.9255 23.3323
Pocillopora_meandrina_HIv1___xfSc0000205 54658 81006 1.4821 3.587
Pocillopora_meandrina_HIv1___xfSc0000206 54623 296109 5.421 8.549
Pocillopora_meandrina_HIv1___xfSc0000212 54299 437761 8.062 11.5408
Pocillopora_meandrina_HIv1___xfSc0000217 54168 468467 8.6484 14.9396
Pocillopora_meandrina_HIv1___xfSc0000223 53823 726609 13.5 12.0416
Pocillopora_meandrina_HIv1___xfSc0000228 53382 670044 12.5519 37.8933
Pocillopora_meandrina_HIv1___xfSc0000237 53049 348855 6.5761 9.984
Pocillopora_meandrina_HIv1___xfSc0000262 52308 345696 6.6089 8.9039
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2430757 46.5092 37.4751
Pocillopora_meandrina_HIv1___xfSc0000272 52107 359607 6.9013 10.8416
Pocillopora_meandrina_HIv1___xfSc0000275 51938 607535 11.6973 14.0092
Pocillopora_meandrina_HIv1___xfSc0000284 51483 689304 13.389 16.9012
Pocillopora_meandrina_HIv1___xfSc0000288 51367 376982 7.339 16.2291
Pocillopora_meandrina_HIv1___xfSc0000300 50845 18294 0.3598 1.5258
Pocillopora_meandrina_HIv1___xfSc0000301 50809 756692 14.8929 13.795
Pocillopora_meandrina_HIv1___xfSc0000343 49544 236122 4.7659 9.7678
Pocillopora_meandrina_HIv1___xfSc0000376 48519 606963 12.5098 39.3223
Pocillopora_meandrina_HIv1___xfSc0000415 47398 366546 7.7334 8.9301
Pocillopora_meandrina_HIv1___xfSc0000423 47202 85448 1.8103 5.0837
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1409006 29.9177 32.7697
Pocillopora_meandrina_HIv1___xfSc0000428 47057 833558 17.7138 25.4028
Pocillopora_meandrina_HIv1___xfSc0000436 46816 428097 9.1442 21.0103
Pocillopora_meandrina_HIv1___xfSc0000445 46561 76306 1.6388 3.8972
Pocillopora_meandrina_HIv1___xfSc0000447 46542 556596 11.959 16.6407
Pocillopora_meandrina_HIv1___xfSc0000469 45938 478281 10.4114 10.2855
Pocillopora_meandrina_HIv1___xfSc0000477 45781 399433 8.7249 9.7121
Pocillopora_meandrina_HIv1___xfSc0000479 45736 216378 4.731 7.1479
Pocillopora_meandrina_HIv1___xfSc0000482 45585 729408 16.0011 28.2116
Pocillopora_meandrina_HIv1___xfSc0000488 45379 291322 6.4198 9.13
Pocillopora_meandrina_HIv1___xfSc0000506 44781 187052 4.177 7.0143
Pocillopora_meandrina_HIv1___xfSc0000527 44235 284084 6.4222 9.8152
Pocillopora_meandrina_HIv1___xfSc0000540 43935 462744 10.5325 14.618
Pocillopora_meandrina_HIv1___xfSc0000555 43535 302735 6.9538 14.978
Pocillopora_meandrina_HIv1___xfSc0000565 43357 499795 11.5274 11.7917
Pocillopora_meandrina_HIv1___xfSc0000566 43316 309319 7.141 11.8596
Pocillopora_meandrina_HIv1___xfSc0000567 43305 241036 5.566 11.7936
Pocillopora_meandrina_HIv1___xfSc0000570 43295 149709 3.4579 9.0477
Pocillopora_meandrina_HIv1___xfSc0000579 43029 93029 2.162 5.489
Pocillopora_meandrina_HIv1___xfSc0000583 42958 450570 10.4886 11.3769
Pocillopora_meandrina_HIv1___xfSc0000596 42675 143745 3.3684 6.3474
Pocillopora_meandrina_HIv1___xfSc0000612 42423 224946 5.3025 8.2489
Pocillopora_meandrina_HIv1___xfSc0000616 42355 3778693 89.2148 248.1258
Pocillopora_meandrina_HIv1___xfSc0000621 42164 377178 8.9455 10.6645
Pocillopora_meandrina_HIv1___xfSc0000642 41754 250994 6.0113 9.2326
Pocillopora_meandrina_HIv1___xfSc0000655 41446 722393 17.4297 36.345
Pocillopora_meandrina_HIv1___xfSc0000692 40426 156317 3.8667 6.1884
Pocillopora_meandrina_HIv1___xfSc0000699 40296 47437 1.1772 2.737
Pocillopora_meandrina_HIv1___xfSc0000704 40233 778344 19.3459 27.5798
Pocillopora_meandrina_HIv1___xfSc0000705 40197 155735 3.8743 8.3958
Pocillopora_meandrina_HIv1___xfSc0000716 39998 449254 11.2319 12.5258
Pocillopora_meandrina_HIv1___xfSc0000725 39827 83700 2.1016 8.1878
Pocillopora_meandrina_HIv1___xfSc0000729 39775 108886 2.7375 24.1508
Pocillopora_meandrina_HIv1___xfSc0000760 39228 24505 0.6247 2.7819
Pocillopora_meandrina_HIv1___xfSc0000763 39151 313017 7.9951 8.1698
Pocillopora_meandrina_HIv1___xfSc0000765 39117 107049 2.7366 5.5184
Pocillopora_meandrina_HIv1___xfSc0000788 38513 337311 8.7584 11.8947
Pocillopora_meandrina_HIv1___xfSc0000811 37888 315345 8.3231 7.9044
Pocillopora_meandrina_HIv1___xfSc0000812 37881 19888 0.525 1.2154
Pocillopora_meandrina_HIv1___xfSc0000817 37779 564652 14.9462 12.3515
Pocillopora_meandrina_HIv1___xfSc0000824 37656 289122 7.678 9.9817
Pocillopora_meandrina_HIv1___xfSc0000835 37434 380736 10.1709 11.8726
Pocillopora_meandrina_HIv1___xfSc0000836 37372 268834 7.1935 11.6877
Pocillopora_meandrina_HIv1___xfSc0000837 37368 205190 5.4911 9.6386
Pocillopora_meandrina_HIv1___xfSc0000840 37283 510846 13.7018 21.9554
Pocillopora_meandrina_HIv1___xfSc0000857 37006 87579 2.3666 5.0557
Pocillopora_meandrina_HIv1___xfSc0000859 36995 65822 1.7792 3.2749
Pocillopora_meandrina_HIv1___xfSc0000866 36925 119122 3.2261 6.483
Pocillopora_meandrina_HIv1___xfSc0000868 36831 179987 4.8868 12.544
Pocillopora_meandrina_HIv1___xfSc0000875 36611 17561 0.4797 1.4285
Pocillopora_meandrina_HIv1___xfSc0000885 36416 190235 5.2239 8.212
Pocillopora_meandrina_HIv1___xfSc0000886 36355 346048 9.5186 15.0226
Pocillopora_meandrina_HIv1___xfSc0000890 36339 257295 7.0804 15.0044
Pocillopora_meandrina_HIv1___xfSc0000892 36267 40773 1.1242 3.448
Pocillopora_meandrina_HIv1___xfSc0000943 35168 9230 0.2625 1.093
Pocillopora_meandrina_HIv1___xfSc0000948 35100 323560 9.2182 11.0043
Pocillopora_meandrina_HIv1___xfSc0000952 34934 105567 3.0219 5.8201
Pocillopora_meandrina_HIv1___xfSc0000953 34905 242497 6.9473 9.2605
Pocillopora_meandrina_HIv1___xfSc0000957 34773 381001 10.9568 18.0937
Pocillopora_meandrina_HIv1___xfSc0000968 34345 17238 0.5019 1.8371
Pocillopora_meandrina_HIv1___xfSc0000974 34140 325564 9.5361 9.992
Pocillopora_meandrina_HIv1___xfSc0000975 33988 516009 15.1821 15.9606
Pocillopora_meandrina_HIv1___xfSc0000995 33324 156305 4.6905 11.3991
Pocillopora_meandrina_HIv1___xfSc0001011 32918 199336 6.0555 12.3407
Pocillopora_meandrina_HIv1___xfSc0001122 29140 363979 12.4907 15.8803
Pocillopora_meandrina_HIv1___xfSc0001170 27381 36575 1.3358 3.6233
Pocillopora_meandrina_HIv1___xfSc0001179 27200 117107 4.3054 7.0437
Pocillopora_meandrina_HIv1___xfSc0001231 22938 19301 0.8414 1.7025
Pocillopora_meandrina_HIv1___xfSc0001237 22715 76038 3.3475 9.1046
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2915119 7.1402 13.0662
Pocillopora_meandrina_HIv1___xpSc0001275 48561 341811 7.0388 12.3372
Pocillopora_meandrina_HIv1___xpSc0001276 38618 150840 3.906 9.1267
Pocillopora_meandrina_HIv1___xpSc0001280 35955 246658 6.8602 10.7444
Pocillopora_meandrina_HIv1___xpSc0001281 34238 277553 8.1066 13.0049
Pocillopora_meandrina_HIv1___xpSc0001290 28931 335058 11.5813 14.1961
Pocillopora_meandrina_HIv1___xpSc0001321 15304 44421 2.9026 6.3095
Pocillopora_meandrina_HIv1___xpSc0001331 8958 124190 13.8636 15.0601
Pocillopora_meandrina_HIv1___xpSc0001337 6786 14910 2.1972 5.2954
Pocillopora_meandrina_HIv1___xpSc0001344 5647 65068 11.5226 17.5029
Pocillopora_meandrina_HIv1___xpSc0001355 3576 64089 17.922 12.951

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
    • 2025/04/23 02:03:31
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