Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-40-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-40-TP3_R1_001.fastp-trim.fq.gz -2 POC-40-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-40-TP3 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:49:40 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-40-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 42,663,376
Mapped reads 42,663,376 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 42,663,376 / 100%
Mapped reads, first in pair 21,331,688 / 50%
Mapped reads, second in pair 21,331,688 / 50%
Mapped reads, both in pair 42,663,376 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.94
Overlapping read pairs 11,929,303 / 55.92%
Duplicated reads (estimated) 4,306,703 / 10.09%
Duplication rate 9.72%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,275,551,667 / 40.31%
Number/percentage of C's 551,280,652 / 9.76%
Number/percentage of T's 2,278,918,693 / 40.37%
Number/percentage of G's 539,576,582 / 9.56%
Number/percentage of N's 431,578 / 0.01%
GC Percentage 19.32%

Coverage

Mean 15.0416
Standard Deviation 15.7928
Mean (paired-end reads overlap ignored) 13.02

Mapping Quality

Mean Mapping Quality 22.38

Insert size

Mean 262.34
Standard Deviation 87.31
P25/Median/P75 197 / 255 / 319

Mismatches and indels

General error rate 21.19%
Mismatches 1,174,680,843
Insertions 8,710,260
Mapped reads with at least one insertion 15.24%
Deletions 6,941,328
Mapped reads with at least one deletion 13.57%
Homopolymer indels 51.82%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 358877014 16.5754 12.6421
Pocillopora_meandrina_HIv1___Sc0000001 21507942 364150580 16.931 11.6904
Pocillopora_meandrina_HIv1___Sc0000002 19741974 324764542 16.4505 11.4383
Pocillopora_meandrina_HIv1___Sc0000003 19417450 280452169 14.4433 12.8575
Pocillopora_meandrina_HIv1___Sc0000004 14584444 215977426 14.8088 20.9362
Pocillopora_meandrina_HIv1___Sc0000005 14098929 221805502 15.7321 10.6536
Pocillopora_meandrina_HIv1___Sc0000006 14068054 224307536 15.9445 14.0602
Pocillopora_meandrina_HIv1___Sc0000007 13590779 215663498 15.8684 12.411
Pocillopora_meandrina_HIv1___Sc0000008 12446599 207541565 16.6746 11.6044
Pocillopora_meandrina_HIv1___Sc0000009 11983232 122032253 10.1836 15.5215
Pocillopora_meandrina_HIv1___Sc0000010 11763137 176983218 15.0456 14.5513
Pocillopora_meandrina_HIv1___Sc0000011 10501528 189712560 18.0652 10.1227
Pocillopora_meandrina_HIv1___Sc0000012 10024633 159872926 15.948 24.1896
Pocillopora_meandrina_HIv1___Sc0000013 9946974 128166810 12.885 11.9767
Pocillopora_meandrina_HIv1___Sc0000014 9536826 161143846 16.897 10.9054
Pocillopora_meandrina_HIv1___Sc0000015 9393205 147139908 15.6645 12.0044
Pocillopora_meandrina_HIv1___Sc0000016 9288165 141941590 15.282 11.7925
Pocillopora_meandrina_HIv1___Sc0000017 9274345 142355996 15.3494 11.4726
Pocillopora_meandrina_HIv1___Sc0000018 8584156 138618358 16.1482 11.2823
Pocillopora_meandrina_HIv1___Sc0000019 7112774 107037553 15.0486 12.3768
Pocillopora_meandrina_HIv1___Sc0000020 6748058 104693580 15.5146 12.3052
Pocillopora_meandrina_HIv1___Sc0000021 6546105 105614820 16.134 11.119
Pocillopora_meandrina_HIv1___Sc0000022 6319256 90343759 14.2966 14.4481
Pocillopora_meandrina_HIv1___Sc0000023 5767069 73849428 12.8054 11.5587
Pocillopora_meandrina_HIv1___Sc0000024 5762297 56610739 9.8243 11.2495
Pocillopora_meandrina_HIv1___Sc0000025 5759531 81778728 14.1989 14.0608
Pocillopora_meandrina_HIv1___Sc0000026 5647578 101985608 18.0583 10.4529
Pocillopora_meandrina_HIv1___Sc0000027 5550630 91294714 16.4476 20.6034
Pocillopora_meandrina_HIv1___Sc0000028 5130920 85328316 16.6302 12.4088
Pocillopora_meandrina_HIv1___Sc0000029 4860867 60032127 12.3501 11.0948
Pocillopora_meandrina_HIv1___Sc0000030 4843735 76870341 15.8701 11.1763
Pocillopora_meandrina_HIv1___Sc0000031 4691590 74015826 15.7763 11.0709
Pocillopora_meandrina_HIv1___Sc0000032 3615800 59935704 16.5761 11.5441
Pocillopora_meandrina_HIv1___Sc0000033 3306609 38701834 11.7044 11.8002
Pocillopora_meandrina_HIv1___Sc0000034 3122802 53878731 17.2533 11.5542
Pocillopora_meandrina_HIv1___Sc0000035 3015365 39471082 13.09 13.4343
Pocillopora_meandrina_HIv1___Sc0000036 3007169 54628567 18.1661 10.1561
Pocillopora_meandrina_HIv1___Sc0000037 2860435 45532716 15.9181 14.3041
Pocillopora_meandrina_HIv1___Sc0000038 2701138 38683329 14.3211 12.8664
Pocillopora_meandrina_HIv1___Sc0000039 2599273 33680880 12.9578 12.4402
Pocillopora_meandrina_HIv1___Sc0000040 2445666 38073682 15.5678 15.0705
Pocillopora_meandrina_HIv1___Sc0000041 2159376 35614307 16.4929 10.8608
Pocillopora_meandrina_HIv1___Sc0000042 1957488 25433659 12.993 10.8254
Pocillopora_meandrina_HIv1___Sc0000043 1845599 23508141 12.7374 10.649
Pocillopora_meandrina_HIv1___Sc0000044 1724711 28181528 16.3399 11.0571
Pocillopora_meandrina_HIv1___Sc0000045 1153740 14144238 12.2595 11.6897
Pocillopora_meandrina_HIv1___Sc0000046 755410 8487140 11.2351 17.218
Pocillopora_meandrina_HIv1___Sc0000047 239089 980943 4.1028 5.4657
Pocillopora_meandrina_HIv1___Sc0000048 214660 82926 0.3863 2.2041
Pocillopora_meandrina_HIv1___Sc0000049 179266 534668 2.9825 7.52
Pocillopora_meandrina_HIv1___Sc0000050 177168 382164 2.1571 5.776
Pocillopora_meandrina_HIv1___Sc0000051 165057 812697 4.9237 7.3739
Pocillopora_meandrina_HIv1___Sc0000052 155210 28894 0.1862 2.0122
Pocillopora_meandrina_HIv1___Sc0000053 123249 201292 1.6332 3.7387
Pocillopora_meandrina_HIv1___Sc0000054 122643 2011867 16.4043 18.9541
Pocillopora_meandrina_HIv1___Sc0000055 121609 898141 7.3855 13.0039
Pocillopora_meandrina_HIv1___Sc0000056 112816 52300 0.4636 4.3621
Pocillopora_meandrina_HIv1___Sc0000057 107171 243975 2.2765 5.1955
Pocillopora_meandrina_HIv1___Sc0000058 98341 28434 0.2891 3.3668
Pocillopora_meandrina_HIv1___Sc0000059 83292 10460 0.1256 0.6125
Pocillopora_meandrina_HIv1___Sc0000060 79483 1060 0.0133 0.1257
Pocillopora_meandrina_HIv1___Sc0000061 75390 368754 4.8913 12.1389
Pocillopora_meandrina_HIv1___Sc0000062 74194 12990 0.1751 0.7812
Pocillopora_meandrina_HIv1___Sc0000063 73457 121291 1.6512 13.9991
Pocillopora_meandrina_HIv1___Sc0000064 72700 16729 0.2301 0.9225
Pocillopora_meandrina_HIv1___Sc0000065 67986 12563 0.1848 1.3531
Pocillopora_meandrina_HIv1___Sc0000066 66659 461926 6.9297 7.4542
Pocillopora_meandrina_HIv1___Sc0000067 64947 162944 2.5089 4.9295
Pocillopora_meandrina_HIv1___Sc0000068 64340 40332 0.6269 1.9962
Pocillopora_meandrina_HIv1___Sc0000069 62616 417033 6.6602 8.3654
Pocillopora_meandrina_HIv1___Sc0000070 60121 264352 4.397 26.3881
Pocillopora_meandrina_HIv1___Sc0000071 57157 90935 1.591 2.9336
Pocillopora_meandrina_HIv1___Sc0000072 56626 17838 0.315 2.9948
Pocillopora_meandrina_HIv1___Sc0000073 56082 18539 0.3306 1.0887
Pocillopora_meandrina_HIv1___Sc0000074 55210 2401 0.0435 0.2851
Pocillopora_meandrina_HIv1___Sc0000075 54685 4170 0.0763 0.3529
Pocillopora_meandrina_HIv1___Sc0000076 54587 179295 3.2846 16.1227
Pocillopora_meandrina_HIv1___Sc0000077 53379 22420 0.42 0.9758
Pocillopora_meandrina_HIv1___Sc0000078 51564 562 0.0109 0.1272
Pocillopora_meandrina_HIv1___Sc0000079 49664 1332 0.0268 0.1745
Pocillopora_meandrina_HIv1___Sc0000080 47218 87697 1.8573 4.7432
Pocillopora_meandrina_HIv1___Sc0000081 42490 10723 0.2524 0.772
Pocillopora_meandrina_HIv1___Sc0000082 32657 635107 19.4478 32.8492
Pocillopora_meandrina_HIv1___Sc0000083 27992 126640 4.5241 2.7379
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 8840580 5.5198 8.9199
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 6780593 5.6613 7.8542
Pocillopora_meandrina_HIv1___xfSc0000002 779520 11006456 14.1195 18.4945
Pocillopora_meandrina_HIv1___xfSc0000003 462347 3226696 6.9789 10.0701
Pocillopora_meandrina_HIv1___xfSc0000004 334777 816830 2.4399 4.67
Pocillopora_meandrina_HIv1___xfSc0000006 290100 751783 2.5915 4.8045
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1016806 4.0308 7.0476
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1541551 10.3964 10.356
Pocillopora_meandrina_HIv1___xfSc0000014 118081 25041 0.2121 0.8074
Pocillopora_meandrina_HIv1___xfSc0000017 98555 373849 3.7933 57.3739
Pocillopora_meandrina_HIv1___xfSc0000021 95778 553989 5.7841 10.0306
Pocillopora_meandrina_HIv1___xfSc0000024 90744 311804 3.4361 6.0594
Pocillopora_meandrina_HIv1___xfSc0000029 85532 132020 1.5435 5.854
Pocillopora_meandrina_HIv1___xfSc0000038 77395 44861 0.5796 3.7816
Pocillopora_meandrina_HIv1___xfSc0000058 69718 614377 8.8123 11.3673
Pocillopora_meandrina_HIv1___xfSc0000059 69426 455292 6.5579 11.2051
Pocillopora_meandrina_HIv1___xfSc0000074 66573 409200 6.1466 7.4152
Pocillopora_meandrina_HIv1___xfSc0000081 65415 650732 9.9477 7.8657
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1531228 23.443 17.8851
Pocillopora_meandrina_HIv1___xfSc0000092 63607 587362 9.2342 6.5102
Pocillopora_meandrina_HIv1___xfSc0000094 62842 309039 4.9177 8.8864
Pocillopora_meandrina_HIv1___xfSc0000113 60556 991483 16.373 15.3611
Pocillopora_meandrina_HIv1___xfSc0000132 59032 445830 7.5523 9.086
Pocillopora_meandrina_HIv1___xfSc0000145 58221 374817 6.4378 6.0495
Pocillopora_meandrina_HIv1___xfSc0000146 58151 512576 8.8146 10.0987
Pocillopora_meandrina_HIv1___xfSc0000168 56681 461013 8.1335 10.0606
Pocillopora_meandrina_HIv1___xfSc0000175 56271 244087 4.3377 10.2071
Pocillopora_meandrina_HIv1___xfSc0000195 55223 112340 2.0343 4.0339
Pocillopora_meandrina_HIv1___xfSc0000199 55095 641089 11.6361 21.4527
Pocillopora_meandrina_HIv1___xfSc0000205 54658 216400 3.9592 5.699
Pocillopora_meandrina_HIv1___xfSc0000206 54623 303398 5.5544 8.9724
Pocillopora_meandrina_HIv1___xfSc0000212 54299 331274 6.1009 9.0109
Pocillopora_meandrina_HIv1___xfSc0000217 54168 491310 9.0701 17.9191
Pocillopora_meandrina_HIv1___xfSc0000223 53823 286415 5.3214 6.8695
Pocillopora_meandrina_HIv1___xfSc0000228 53382 430987 8.0736 20.8899
Pocillopora_meandrina_HIv1___xfSc0000237 53049 361681 6.8179 6.8599
Pocillopora_meandrina_HIv1___xfSc0000262 52308 428445 8.1908 8.6743
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2933602 56.1305 59.4944
Pocillopora_meandrina_HIv1___xfSc0000272 52107 342006 6.5635 8.6953
Pocillopora_meandrina_HIv1___xfSc0000275 51938 740168 14.251 15.9691
Pocillopora_meandrina_HIv1___xfSc0000284 51483 837594 16.2693 18.3925
Pocillopora_meandrina_HIv1___xfSc0000288 51367 286330 5.5742 13.1193
Pocillopora_meandrina_HIv1___xfSc0000300 50845 13203 0.2597 0.7941
Pocillopora_meandrina_HIv1___xfSc0000301 50809 572993 11.2774 9.0474
Pocillopora_meandrina_HIv1___xfSc0000343 49544 237596 4.7957 8.4454
Pocillopora_meandrina_HIv1___xfSc0000376 48519 445925 9.1907 23.0521
Pocillopora_meandrina_HIv1___xfSc0000415 47398 420479 8.8712 8.605
Pocillopora_meandrina_HIv1___xfSc0000423 47202 85930 1.8205 4.6463
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1653071 35.1 35.1302
Pocillopora_meandrina_HIv1___xfSc0000428 47057 267623 5.6872 10.2447
Pocillopora_meandrina_HIv1___xfSc0000436 46816 568075 12.1342 18.3734
Pocillopora_meandrina_HIv1___xfSc0000445 46561 203080 4.3616 5.1204
Pocillopora_meandrina_HIv1___xfSc0000447 46542 526200 11.3059 11.5735
Pocillopora_meandrina_HIv1___xfSc0000469 45938 434563 9.4598 7.0876
Pocillopora_meandrina_HIv1___xfSc0000477 45781 268477 5.8644 5.9958
Pocillopora_meandrina_HIv1___xfSc0000479 45736 201635 4.4087 6.6679
Pocillopora_meandrina_HIv1___xfSc0000482 45585 471874 10.3515 14.6773
Pocillopora_meandrina_HIv1___xfSc0000488 45379 158628 3.4956 5.4132
Pocillopora_meandrina_HIv1___xfSc0000506 44781 525731 11.74 18.2247
Pocillopora_meandrina_HIv1___xfSc0000527 44235 280671 6.345 7.6967
Pocillopora_meandrina_HIv1___xfSc0000540 43935 421906 9.603 12.225
Pocillopora_meandrina_HIv1___xfSc0000555 43535 336214 7.7228 11.8103
Pocillopora_meandrina_HIv1___xfSc0000565 43357 296188 6.8314 6.0925
Pocillopora_meandrina_HIv1___xfSc0000566 43316 274219 6.3307 7.5795
Pocillopora_meandrina_HIv1___xfSc0000567 43305 143963 3.3244 6.3363
Pocillopora_meandrina_HIv1___xfSc0000570 43295 408921 9.445 12.6244
Pocillopora_meandrina_HIv1___xfSc0000579 43029 118922 2.7638 5.4241
Pocillopora_meandrina_HIv1___xfSc0000583 42958 325647 7.5806 8.6564
Pocillopora_meandrina_HIv1___xfSc0000596 42675 252295 5.912 8.2883
Pocillopora_meandrina_HIv1___xfSc0000612 42423 277980 6.5526 7.43
Pocillopora_meandrina_HIv1___xfSc0000616 42355 9450359 223.1226 736.0143
Pocillopora_meandrina_HIv1___xfSc0000621 42164 306012 7.2577 8.6973
Pocillopora_meandrina_HIv1___xfSc0000642 41754 177204 4.244 7.8786
Pocillopora_meandrina_HIv1___xfSc0000655 41446 350908 8.4666 16.2162
Pocillopora_meandrina_HIv1___xfSc0000692 40426 264380 6.5399 7.9169
Pocillopora_meandrina_HIv1___xfSc0000699 40296 34596 0.8585 1.8929
Pocillopora_meandrina_HIv1___xfSc0000704 40233 394393 9.8027 12.1707
Pocillopora_meandrina_HIv1___xfSc0000705 40197 206898 5.1471 6.9367
Pocillopora_meandrina_HIv1___xfSc0000716 39998 268198 6.7053 7.685
Pocillopora_meandrina_HIv1___xfSc0000725 39827 199357 5.0056 11.6593
Pocillopora_meandrina_HIv1___xfSc0000729 39775 46249 1.1628 8.9203
Pocillopora_meandrina_HIv1___xfSc0000760 39228 25434 0.6484 1.7061
Pocillopora_meandrina_HIv1___xfSc0000763 39151 387115 9.8877 6.6642
Pocillopora_meandrina_HIv1___xfSc0000765 39117 207166 5.2961 7.8351
Pocillopora_meandrina_HIv1___xfSc0000788 38513 559563 14.5292 12.3766
Pocillopora_meandrina_HIv1___xfSc0000811 37888 440608 11.6292 7.8614
Pocillopora_meandrina_HIv1___xfSc0000812 37881 32227 0.8507 1.6242
Pocillopora_meandrina_HIv1___xfSc0000817 37779 381228 10.091 7.1665
Pocillopora_meandrina_HIv1___xfSc0000824 37656 239554 6.3616 10.3423
Pocillopora_meandrina_HIv1___xfSc0000835 37434 346028 9.2437 11.4532
Pocillopora_meandrina_HIv1___xfSc0000836 37372 261370 6.9937 10.1853
Pocillopora_meandrina_HIv1___xfSc0000837 37368 395933 10.5955 9.8869
Pocillopora_meandrina_HIv1___xfSc0000840 37283 246472 6.6108 15.1879
Pocillopora_meandrina_HIv1___xfSc0000857 37006 142781 3.8583 5.3094
Pocillopora_meandrina_HIv1___xfSc0000859 36995 54451 1.4718 3.6254
Pocillopora_meandrina_HIv1___xfSc0000866 36925 70912 1.9204 2.889
Pocillopora_meandrina_HIv1___xfSc0000868 36831 166931 4.5324 9.125
Pocillopora_meandrina_HIv1___xfSc0000875 36611 54831 1.4977 2.9924
Pocillopora_meandrina_HIv1___xfSc0000885 36416 190350 5.2271 6.6129
Pocillopora_meandrina_HIv1___xfSc0000886 36355 104492 2.8742 4.2434
Pocillopora_meandrina_HIv1___xfSc0000890 36339 236242 6.5011 12.1057
Pocillopora_meandrina_HIv1___xfSc0000892 36267 135131 3.726 22.1207
Pocillopora_meandrina_HIv1___xfSc0000943 35168 12814 0.3644 1.19
Pocillopora_meandrina_HIv1___xfSc0000948 35100 354661 10.1043 10.2251
Pocillopora_meandrina_HIv1___xfSc0000952 34934 458994 13.1389 8.7366
Pocillopora_meandrina_HIv1___xfSc0000953 34905 146192 4.1883 5.4225
Pocillopora_meandrina_HIv1___xfSc0000957 34773 162543 4.6744 8.1933
Pocillopora_meandrina_HIv1___xfSc0000968 34345 38892 1.1324 2.9799
Pocillopora_meandrina_HIv1___xfSc0000974 34140 375297 10.9929 10.4499
Pocillopora_meandrina_HIv1___xfSc0000975 33988 249598 7.3437 7.5819
Pocillopora_meandrina_HIv1___xfSc0000995 33324 99289 2.9795 7.1686
Pocillopora_meandrina_HIv1___xfSc0001011 32918 454876 13.8185 13.8807
Pocillopora_meandrina_HIv1___xfSc0001122 29140 323611 11.1054 8.7926
Pocillopora_meandrina_HIv1___xfSc0001170 27381 57537 2.1013 3.5211
Pocillopora_meandrina_HIv1___xfSc0001179 27200 112340 4.1301 6.7643
Pocillopora_meandrina_HIv1___xfSc0001231 22938 20143 0.8781 1.3901
Pocillopora_meandrina_HIv1___xfSc0001237 22715 178171 7.8438 18.6055
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3302254 8.0884 9.4344
Pocillopora_meandrina_HIv1___xpSc0001275 48561 186138 3.8331 7.2545
Pocillopora_meandrina_HIv1___xpSc0001276 38618 176498 4.5704 11.5411
Pocillopora_meandrina_HIv1___xpSc0001280 35955 148842 4.1397 7.713
Pocillopora_meandrina_HIv1___xpSc0001281 34238 289151 8.4453 12.2073
Pocillopora_meandrina_HIv1___xpSc0001290 28931 234704 8.1125 6.5951
Pocillopora_meandrina_HIv1___xpSc0001321 15304 59863 3.9116 8.4783
Pocillopora_meandrina_HIv1___xpSc0001331 8958 151021 16.8588 11.4877
Pocillopora_meandrina_HIv1___xpSc0001337 6786 84679 12.4785 8.0683
Pocillopora_meandrina_HIv1___xpSc0001344 5647 63280 11.206 13.8085
Pocillopora_meandrina_HIv1___xpSc0001355 3576 42140 11.7841 8.8418

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 20:49:42
    Generated by QualiMap v.2.3