Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-53-TP3.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-53-TP3_R1_001.fastp-trim.fq.gz -2 POC-53-TP3_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-53-TP3 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:31:58 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-53-TP3.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 45,025,550
Mapped reads 45,025,550 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 45,025,550 / 100%
Mapped reads, first in pair 22,512,775 / 50%
Mapped reads, second in pair 22,512,775 / 50%
Mapped reads, both in pair 45,025,550 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.67
Overlapping read pairs 13,421,090 / 59.62%
Duplicated reads (estimated) 4,985,482 / 11.07%
Duplication rate 10.69%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,377,526,395 / 40.28%
Number/percentage of C's 577,664,970 / 9.79%
Number/percentage of T's 2,380,346,327 / 40.33%
Number/percentage of G's 565,857,939 / 9.59%
Number/percentage of N's 537,050 / 0.01%
GC Percentage 19.38%

Coverage

Mean 15.7234
Standard Deviation 15.3631
Mean (paired-end reads overlap ignored) 13.31

Mapping Quality

Mean Mapping Quality 22.57

Insert size

Mean 251.84
Standard Deviation 89.64
P25/Median/P75 183 / 246 / 311

Mismatches and indels

General error rate 21.22%
Mismatches 1,229,738,780
Insertions 8,948,747
Mapped reads with at least one insertion 14.92%
Deletions 7,160,338
Mapped reads with at least one deletion 13.3%
Homopolymer indels 52.01%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 363496483 16.7888 12.1088
Pocillopora_meandrina_HIv1___Sc0000001 21507942 379753301 17.6564 11.3646
Pocillopora_meandrina_HIv1___Sc0000002 19741974 340024616 17.2234 11.8463
Pocillopora_meandrina_HIv1___Sc0000003 19417450 304479635 15.6807 13.3558
Pocillopora_meandrina_HIv1___Sc0000004 14584444 221666591 15.1988 19.842
Pocillopora_meandrina_HIv1___Sc0000005 14098929 235257926 16.6862 11.6899
Pocillopora_meandrina_HIv1___Sc0000006 14068054 233684211 16.611 12.1029
Pocillopora_meandrina_HIv1___Sc0000007 13590779 222574960 16.3769 13.2023
Pocillopora_meandrina_HIv1___Sc0000008 12446599 216109931 17.363 12.4652
Pocillopora_meandrina_HIv1___Sc0000009 11983232 110584133 9.2282 14.1769
Pocillopora_meandrina_HIv1___Sc0000010 11763137 188536350 16.0277 14.6279
Pocillopora_meandrina_HIv1___Sc0000011 10501528 198252914 18.8785 10.3787
Pocillopora_meandrina_HIv1___Sc0000012 10024633 169245410 16.883 21.5697
Pocillopora_meandrina_HIv1___Sc0000013 9946974 131683761 13.2386 12.2274
Pocillopora_meandrina_HIv1___Sc0000014 9536826 167356837 17.5485 11.3464
Pocillopora_meandrina_HIv1___Sc0000015 9393205 154874283 16.4879 12.2094
Pocillopora_meandrina_HIv1___Sc0000016 9288165 150963811 16.2534 12.3914
Pocillopora_meandrina_HIv1___Sc0000017 9274345 150923066 16.2732 11.9344
Pocillopora_meandrina_HIv1___Sc0000018 8584156 147564217 17.1903 11.7611
Pocillopora_meandrina_HIv1___Sc0000019 7112774 113529700 15.9614 12.6791
Pocillopora_meandrina_HIv1___Sc0000020 6748058 110368394 16.3556 13.7117
Pocillopora_meandrina_HIv1___Sc0000021 6546105 113301639 17.3083 12.0917
Pocillopora_meandrina_HIv1___Sc0000022 6319256 97761196 15.4704 15.8475
Pocillopora_meandrina_HIv1___Sc0000023 5767069 82763531 14.3511 13.3233
Pocillopora_meandrina_HIv1___Sc0000024 5762297 61448014 10.6638 12.4413
Pocillopora_meandrina_HIv1___Sc0000025 5759531 80944397 14.054 14.0296
Pocillopora_meandrina_HIv1___Sc0000026 5647578 105889024 18.7495 10.7437
Pocillopora_meandrina_HIv1___Sc0000027 5550630 85896390 15.4751 18.6009
Pocillopora_meandrina_HIv1___Sc0000028 5130920 91554474 17.8437 13.6077
Pocillopora_meandrina_HIv1___Sc0000029 4860867 68607977 14.1143 11.7127
Pocillopora_meandrina_HIv1___Sc0000030 4843735 80594736 16.639 10.4195
Pocillopora_meandrina_HIv1___Sc0000031 4691590 78082849 16.6432 11.5495
Pocillopora_meandrina_HIv1___Sc0000032 3615800 66051240 18.2674 12.8069
Pocillopora_meandrina_HIv1___Sc0000033 3306609 41544626 12.5641 11.8952
Pocillopora_meandrina_HIv1___Sc0000034 3122802 53288285 17.0643 11.4849
Pocillopora_meandrina_HIv1___Sc0000035 3015365 42258510 14.0144 13.5283
Pocillopora_meandrina_HIv1___Sc0000036 3007169 56657685 18.8409 10.5072
Pocillopora_meandrina_HIv1___Sc0000037 2860435 51611104 18.0431 16.4606
Pocillopora_meandrina_HIv1___Sc0000038 2701138 45660029 16.904 14.3999
Pocillopora_meandrina_HIv1___Sc0000039 2599273 33575731 12.9174 12.2423
Pocillopora_meandrina_HIv1___Sc0000040 2445666 40636602 16.6158 16.0303
Pocillopora_meandrina_HIv1___Sc0000041 2159376 36763496 17.0251 11.2188
Pocillopora_meandrina_HIv1___Sc0000042 1957488 25751540 13.1554 11.4267
Pocillopora_meandrina_HIv1___Sc0000043 1845599 25089876 13.5944 11.258
Pocillopora_meandrina_HIv1___Sc0000044 1724711 29868817 17.3182 12.1028
Pocillopora_meandrina_HIv1___Sc0000045 1153740 14185709 12.2954 11.5359
Pocillopora_meandrina_HIv1___Sc0000046 755410 8610554 11.3985 15.2195
Pocillopora_meandrina_HIv1___Sc0000047 239089 2156176 9.0183 11.5689
Pocillopora_meandrina_HIv1___Sc0000048 214660 86500 0.403 2.2481
Pocillopora_meandrina_HIv1___Sc0000049 179266 506942 2.8279 7.9679
Pocillopora_meandrina_HIv1___Sc0000050 177168 227921 1.2865 3.5552
Pocillopora_meandrina_HIv1___Sc0000051 165057 930973 5.6403 8.2026
Pocillopora_meandrina_HIv1___Sc0000052 155210 74968 0.483 5.2663
Pocillopora_meandrina_HIv1___Sc0000053 123249 322466 2.6164 5.9212
Pocillopora_meandrina_HIv1___Sc0000054 122643 1835344 14.9649 14.0469
Pocillopora_meandrina_HIv1___Sc0000055 121609 709581 5.8349 11.1036
Pocillopora_meandrina_HIv1___Sc0000056 112816 69329 0.6145 5.2712
Pocillopora_meandrina_HIv1___Sc0000057 107171 415473 3.8767 9.0225
Pocillopora_meandrina_HIv1___Sc0000058 98341 75912 0.7719 8.5362
Pocillopora_meandrina_HIv1___Sc0000059 83292 8135 0.0977 0.4354
Pocillopora_meandrina_HIv1___Sc0000060 79483 1081 0.0136 0.1405
Pocillopora_meandrina_HIv1___Sc0000061 75390 202532 2.6865 6.2893
Pocillopora_meandrina_HIv1___Sc0000062 74194 17105 0.2305 1.0629
Pocillopora_meandrina_HIv1___Sc0000063 73457 57740 0.786 8.5169
Pocillopora_meandrina_HIv1___Sc0000064 72700 8546 0.1176 0.4738
Pocillopora_meandrina_HIv1___Sc0000065 67986 11905 0.1751 1.3516
Pocillopora_meandrina_HIv1___Sc0000066 66659 448381 6.7265 7.0534
Pocillopora_meandrina_HIv1___Sc0000067 64947 166354 2.5614 4.8775
Pocillopora_meandrina_HIv1___Sc0000068 64340 33028 0.5133 1.5798
Pocillopora_meandrina_HIv1___Sc0000069 62616 383069 6.1177 7.7423
Pocillopora_meandrina_HIv1___Sc0000070 60121 150552 2.5041 12.1296
Pocillopora_meandrina_HIv1___Sc0000071 57157 66995 1.1721 2.3591
Pocillopora_meandrina_HIv1___Sc0000072 56626 14302 0.2526 2.6413
Pocillopora_meandrina_HIv1___Sc0000073 56082 7938 0.1415 0.4682
Pocillopora_meandrina_HIv1___Sc0000074 55210 1685 0.0305 0.2095
Pocillopora_meandrina_HIv1___Sc0000075 54685 2246 0.0411 0.2302
Pocillopora_meandrina_HIv1___Sc0000076 54587 201990 3.7003 18.739
Pocillopora_meandrina_HIv1___Sc0000077 53379 20752 0.3888 0.9482
Pocillopora_meandrina_HIv1___Sc0000078 51564 1577 0.0306 0.2142
Pocillopora_meandrina_HIv1___Sc0000079 49664 3889 0.0783 0.3654
Pocillopora_meandrina_HIv1___Sc0000080 47218 111234 2.3558 5.9901
Pocillopora_meandrina_HIv1___Sc0000081 42490 17056 0.4014 1.1375
Pocillopora_meandrina_HIv1___Sc0000082 32657 675065 20.6714 39.8578
Pocillopora_meandrina_HIv1___Sc0000083 27992 112591 4.0223 2.5806
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 12093472 7.5508 11.4152
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 6565959 5.4821 9.1651
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5726073 7.3456 9.8785
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2082925 4.5051 6.4797
Pocillopora_meandrina_HIv1___xfSc0000004 334777 879909 2.6283 4.9685
Pocillopora_meandrina_HIv1___xfSc0000006 290100 781315 2.6933 4.8925
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2655703 10.5277 15.4664
Pocillopora_meandrina_HIv1___xfSc0000012 148278 916236 6.1792 8.7598
Pocillopora_meandrina_HIv1___xfSc0000014 118081 26062 0.2207 0.8154
Pocillopora_meandrina_HIv1___xfSc0000017 98555 380447 3.8603 57.5053
Pocillopora_meandrina_HIv1___xfSc0000021 95778 645366 6.7381 11.4218
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1003171 11.055 15.9272
Pocillopora_meandrina_HIv1___xfSc0000029 85532 212163 2.4805 6.414
Pocillopora_meandrina_HIv1___xfSc0000038 77395 21385 0.2763 1.6411
Pocillopora_meandrina_HIv1___xfSc0000058 69718 810017 11.6185 11.3257
Pocillopora_meandrina_HIv1___xfSc0000059 69426 596289 8.5888 10.8128
Pocillopora_meandrina_HIv1___xfSc0000074 66573 527734 7.9271 6.8454
Pocillopora_meandrina_HIv1___xfSc0000081 65415 545227 8.3349 6.876
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1193988 18.2799 13.0475
Pocillopora_meandrina_HIv1___xfSc0000092 63607 783891 12.324 11.2294
Pocillopora_meandrina_HIv1___xfSc0000094 62842 109180 1.7374 3.5556
Pocillopora_meandrina_HIv1___xfSc0000113 60556 676659 11.1741 8.5896
Pocillopora_meandrina_HIv1___xfSc0000132 59032 467761 7.9239 9.9776
Pocillopora_meandrina_HIv1___xfSc0000145 58221 365816 6.2832 6.4958
Pocillopora_meandrina_HIv1___xfSc0000146 58151 412792 7.0986 8.8426
Pocillopora_meandrina_HIv1___xfSc0000168 56681 394576 6.9613 8.6555
Pocillopora_meandrina_HIv1___xfSc0000175 56271 262158 4.6588 12.0559
Pocillopora_meandrina_HIv1___xfSc0000195 55223 99974 1.8104 3.4592
Pocillopora_meandrina_HIv1___xfSc0000199 55095 258132 4.6852 10.0414
Pocillopora_meandrina_HIv1___xfSc0000205 54658 477108 8.729 9.6384
Pocillopora_meandrina_HIv1___xfSc0000206 54623 304061 5.5665 9.2492
Pocillopora_meandrina_HIv1___xfSc0000212 54299 342766 6.3126 9.5205
Pocillopora_meandrina_HIv1___xfSc0000217 54168 573355 10.5848 21.8704
Pocillopora_meandrina_HIv1___xfSc0000223 53823 369622 6.8674 7.7433
Pocillopora_meandrina_HIv1___xfSc0000228 53382 373114 6.9895 26.8367
Pocillopora_meandrina_HIv1___xfSc0000237 53049 349666 6.5914 7.589
Pocillopora_meandrina_HIv1___xfSc0000262 52308 383908 7.3394 7.4104
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2168512 41.4915 48.7184
Pocillopora_meandrina_HIv1___xfSc0000272 52107 378798 7.2696 9.0599
Pocillopora_meandrina_HIv1___xfSc0000275 51938 463973 8.9332 9.8402
Pocillopora_meandrina_HIv1___xfSc0000284 51483 621820 12.0782 13.1441
Pocillopora_meandrina_HIv1___xfSc0000288 51367 443490 8.6338 12.6024
Pocillopora_meandrina_HIv1___xfSc0000300 50845 5946 0.1169 0.4995
Pocillopora_meandrina_HIv1___xfSc0000301 50809 465190 9.1557 10.9225
Pocillopora_meandrina_HIv1___xfSc0000343 49544 286519 5.7831 7.9616
Pocillopora_meandrina_HIv1___xfSc0000376 48519 550079 11.3374 34.2383
Pocillopora_meandrina_HIv1___xfSc0000415 47398 145015 3.0595 4.8788
Pocillopora_meandrina_HIv1___xfSc0000423 47202 74356 1.5753 3.7188
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1557743 33.0759 31.4434
Pocillopora_meandrina_HIv1___xfSc0000428 47057 665587 14.1443 23.7738
Pocillopora_meandrina_HIv1___xfSc0000436 46816 571104 12.1989 17.9762
Pocillopora_meandrina_HIv1___xfSc0000445 46561 460515 9.8906 9.2383
Pocillopora_meandrina_HIv1___xfSc0000447 46542 619370 13.3078 12.6165
Pocillopora_meandrina_HIv1___xfSc0000469 45938 558101 12.149 8.8212
Pocillopora_meandrina_HIv1___xfSc0000477 45781 312917 6.8351 7.2489
Pocillopora_meandrina_HIv1___xfSc0000479 45736 184160 4.0266 6.4241
Pocillopora_meandrina_HIv1___xfSc0000482 45585 399271 8.7588 12.3174
Pocillopora_meandrina_HIv1___xfSc0000488 45379 256692 5.6566 7.7771
Pocillopora_meandrina_HIv1___xfSc0000506 44781 266654 5.9546 8.1714
Pocillopora_meandrina_HIv1___xfSc0000527 44235 326373 7.3782 9.0261
Pocillopora_meandrina_HIv1___xfSc0000540 43935 463503 10.5497 14.4857
Pocillopora_meandrina_HIv1___xfSc0000555 43535 381274 8.7579 14.671
Pocillopora_meandrina_HIv1___xfSc0000565 43357 579939 13.3759 11.3472
Pocillopora_meandrina_HIv1___xfSc0000566 43316 310545 7.1693 9.5611
Pocillopora_meandrina_HIv1___xfSc0000567 43305 182960 4.2249 8.1377
Pocillopora_meandrina_HIv1___xfSc0000570 43295 208209 4.8091 6.8466
Pocillopora_meandrina_HIv1___xfSc0000579 43029 78638 1.8276 3.7679
Pocillopora_meandrina_HIv1___xfSc0000583 42958 318592 7.4164 8.4574
Pocillopora_meandrina_HIv1___xfSc0000596 42675 220397 5.1645 8.5788
Pocillopora_meandrina_HIv1___xfSc0000612 42423 369371 8.7069 8.3791
Pocillopora_meandrina_HIv1___xfSc0000616 42355 8237851 194.4954 655.7458
Pocillopora_meandrina_HIv1___xfSc0000621 42164 288342 6.8386 8.3513
Pocillopora_meandrina_HIv1___xfSc0000642 41754 215989 5.1729 7.6773
Pocillopora_meandrina_HIv1___xfSc0000655 41446 385263 9.2955 20.9781
Pocillopora_meandrina_HIv1___xfSc0000692 40426 54263 1.3423 4.144
Pocillopora_meandrina_HIv1___xfSc0000699 40296 43773 1.0863 2.6149
Pocillopora_meandrina_HIv1___xfSc0000704 40233 655015 16.2805 20.9437
Pocillopora_meandrina_HIv1___xfSc0000705 40197 181541 4.5163 6.4024
Pocillopora_meandrina_HIv1___xfSc0000716 39998 309555 7.7393 8.7762
Pocillopora_meandrina_HIv1___xfSc0000725 39827 326770 8.2047 18.3037
Pocillopora_meandrina_HIv1___xfSc0000729 39775 11836 0.2976 1.8269
Pocillopora_meandrina_HIv1___xfSc0000760 39228 12058 0.3074 0.9163
Pocillopora_meandrina_HIv1___xfSc0000763 39151 351581 8.9801 6.5461
Pocillopora_meandrina_HIv1___xfSc0000765 39117 178339 4.5591 7.167
Pocillopora_meandrina_HIv1___xfSc0000788 38513 584959 15.1886 16.182
Pocillopora_meandrina_HIv1___xfSc0000811 37888 320275 8.4532 8.5564
Pocillopora_meandrina_HIv1___xfSc0000812 37881 18841 0.4974 1.1194
Pocillopora_meandrina_HIv1___xfSc0000817 37779 486066 12.866 7.6398
Pocillopora_meandrina_HIv1___xfSc0000824 37656 49709 1.3201 2.1819
Pocillopora_meandrina_HIv1___xfSc0000835 37434 373972 9.9902 9.5798
Pocillopora_meandrina_HIv1___xfSc0000836 37372 229969 6.1535 9.5104
Pocillopora_meandrina_HIv1___xfSc0000837 37368 97491 2.6089 5.1586
Pocillopora_meandrina_HIv1___xfSc0000840 37283 239582 6.426 15.6875
Pocillopora_meandrina_HIv1___xfSc0000857 37006 121839 3.2924 4.6182
Pocillopora_meandrina_HIv1___xfSc0000859 36995 63741 1.723 3.6254
Pocillopora_meandrina_HIv1___xfSc0000866 36925 106732 2.8905 4.8037
Pocillopora_meandrina_HIv1___xfSc0000868 36831 124567 3.3821 7.5884
Pocillopora_meandrina_HIv1___xfSc0000875 36611 72343 1.976 4.7653
Pocillopora_meandrina_HIv1___xfSc0000885 36416 208040 5.7129 7.4745
Pocillopora_meandrina_HIv1___xfSc0000886 36355 184362 5.0712 8.0443
Pocillopora_meandrina_HIv1___xfSc0000890 36339 256385 7.0554 10.9438
Pocillopora_meandrina_HIv1___xfSc0000892 36267 96555 2.6623 11.587
Pocillopora_meandrina_HIv1___xfSc0000943 35168 9110 0.259 1.2218
Pocillopora_meandrina_HIv1___xfSc0000948 35100 323383 9.2132 9.8832
Pocillopora_meandrina_HIv1___xfSc0000952 34934 241098 6.9015 7.1356
Pocillopora_meandrina_HIv1___xfSc0000953 34905 143858 4.1214 5.227
Pocillopora_meandrina_HIv1___xfSc0000957 34773 262036 7.5356 9.9409
Pocillopora_meandrina_HIv1___xfSc0000968 34345 43601 1.2695 3.2039
Pocillopora_meandrina_HIv1___xfSc0000974 34140 350932 10.2792 9.1497
Pocillopora_meandrina_HIv1___xfSc0000975 33988 318631 9.3748 8.9865
Pocillopora_meandrina_HIv1___xfSc0000995 33324 87340 2.6209 5.9705
Pocillopora_meandrina_HIv1___xfSc0001011 32918 376485 11.4371 12.8349
Pocillopora_meandrina_HIv1___xfSc0001122 29140 281227 9.6509 11.7514
Pocillopora_meandrina_HIv1___xfSc0001170 27381 48834 1.7835 5.3295
Pocillopora_meandrina_HIv1___xfSc0001179 27200 95705 3.5186 6.305
Pocillopora_meandrina_HIv1___xfSc0001231 22938 20853 0.9091 1.5473
Pocillopora_meandrina_HIv1___xfSc0001237 22715 177875 7.8307 18.1108
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2895910 7.0931 10.4128
Pocillopora_meandrina_HIv1___xpSc0001275 48561 168309 3.4659 7.0637
Pocillopora_meandrina_HIv1___xpSc0001276 38618 81939 2.1218 5.6052
Pocillopora_meandrina_HIv1___xpSc0001280 35955 202649 5.6362 8.1769
Pocillopora_meandrina_HIv1___xpSc0001281 34238 268245 7.8347 11.2228
Pocillopora_meandrina_HIv1___xpSc0001290 28931 431473 14.9139 10.8366
Pocillopora_meandrina_HIv1___xpSc0001321 15304 37882 2.4753 4.5538
Pocillopora_meandrina_HIv1___xpSc0001331 8958 197226 22.0167 9.8136
Pocillopora_meandrina_HIv1___xpSc0001337 6786 28577 4.2112 8.1393
Pocillopora_meandrina_HIv1___xpSc0001344 5647 66260 11.7337 14.5264
Pocillopora_meandrina_HIv1___xpSc0001355 3576 38705 10.8235 8.9773

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 21:32:08
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