Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-40-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-40-TP1_R1_001.fastp-trim.fq.gz -2 POC-40-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-40-TP1 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:06:38 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-40-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 40,379,014
Mapped reads 40,379,014 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 40,379,014 / 100%
Mapped reads, first in pair 20,189,507 / 50%
Mapped reads, second in pair 20,189,507 / 50%
Mapped reads, both in pair 40,379,014 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.94
Overlapping read pairs 10,493,721 / 51.98%
Duplicated reads (estimated) 3,932,666 / 9.74%
Duplication rate 9.5%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,153,878,266 / 40.3%
Number/percentage of C's 521,781,293 / 9.76%
Number/percentage of T's 2,156,669,463 / 40.36%
Number/percentage of G's 511,194,053 / 9.57%
Number/percentage of N's 444,676 / 0.01%
GC Percentage 19.33%

Coverage

Mean 14.2363
Standard Deviation 12.9829
Mean (paired-end reads overlap ignored) 12.48

Mapping Quality

Mean Mapping Quality 22.64

Insert size

Mean 269.82
Standard Deviation 89.73
P25/Median/P75 203 / 264 / 330

Mismatches and indels

General error rate 21.16%
Mismatches 1,110,750,859
Insertions 7,956,554
Mapped reads with at least one insertion 14.78%
Deletions 6,327,675
Mapped reads with at least one deletion 13.13%
Homopolymer indels 52.08%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 340440785 15.7239 11.5876
Pocillopora_meandrina_HIv1___Sc0000001 21507942 345604781 16.0687 11.1551
Pocillopora_meandrina_HIv1___Sc0000002 19741974 313825784 15.8964 10.9903
Pocillopora_meandrina_HIv1___Sc0000003 19417450 264678856 13.631 12.3298
Pocillopora_meandrina_HIv1___Sc0000004 14584444 201589978 13.8223 17.3303
Pocillopora_meandrina_HIv1___Sc0000005 14098929 214991729 15.2488 10.2429
Pocillopora_meandrina_HIv1___Sc0000006 14068054 214836751 15.2712 13.1756
Pocillopora_meandrina_HIv1___Sc0000007 13590779 203999156 15.0101 11.728
Pocillopora_meandrina_HIv1___Sc0000008 12446599 202289957 16.2526 11.1003
Pocillopora_meandrina_HIv1___Sc0000009 11983232 110121034 9.1896 14.1544
Pocillopora_meandrina_HIv1___Sc0000010 11763137 165925455 14.1055 13.1798
Pocillopora_meandrina_HIv1___Sc0000011 10501528 183898706 17.5116 9.7538
Pocillopora_meandrina_HIv1___Sc0000012 10024633 145400036 14.5043 14.0945
Pocillopora_meandrina_HIv1___Sc0000013 9946974 116895707 11.7519 11.2879
Pocillopora_meandrina_HIv1___Sc0000014 9536826 155498050 16.305 10.4506
Pocillopora_meandrina_HIv1___Sc0000015 9393205 141601166 15.0749 11.6077
Pocillopora_meandrina_HIv1___Sc0000016 9288165 135078463 14.5431 11.1987
Pocillopora_meandrina_HIv1___Sc0000017 9274345 136245045 14.6905 10.9796
Pocillopora_meandrina_HIv1___Sc0000018 8584156 132881710 15.4799 10.8652
Pocillopora_meandrina_HIv1___Sc0000019 7112774 101868344 14.3219 11.6626
Pocillopora_meandrina_HIv1___Sc0000020 6748058 98892295 14.6549 11.5438
Pocillopora_meandrina_HIv1___Sc0000021 6546105 102361238 15.637 10.7085
Pocillopora_meandrina_HIv1___Sc0000022 6319256 84614279 13.3899 13.5191
Pocillopora_meandrina_HIv1___Sc0000023 5767069 70812378 12.2787 11.1044
Pocillopora_meandrina_HIv1___Sc0000024 5762297 51290717 8.9011 10.6221
Pocillopora_meandrina_HIv1___Sc0000025 5759531 77484232 13.4532 13.6552
Pocillopora_meandrina_HIv1___Sc0000026 5647578 98338694 17.4125 10.1605
Pocillopora_meandrina_HIv1___Sc0000027 5550630 85771958 15.4527 19.5493
Pocillopora_meandrina_HIv1___Sc0000028 5130920 80944123 15.7758 11.8956
Pocillopora_meandrina_HIv1___Sc0000029 4860867 58259239 11.9854 10.7661
Pocillopora_meandrina_HIv1___Sc0000030 4843735 73804997 15.2372 10.0985
Pocillopora_meandrina_HIv1___Sc0000031 4691590 71329513 15.2037 10.4375
Pocillopora_meandrina_HIv1___Sc0000032 3615800 57397006 15.8739 11.0438
Pocillopora_meandrina_HIv1___Sc0000033 3306609 36890620 11.1566 10.9829
Pocillopora_meandrina_HIv1___Sc0000034 3122802 50759664 16.2545 10.9476
Pocillopora_meandrina_HIv1___Sc0000035 3015365 36255535 12.0236 12.6513
Pocillopora_meandrina_HIv1___Sc0000036 3007169 53794596 17.8888 10.0013
Pocillopora_meandrina_HIv1___Sc0000037 2860435 43971844 15.3724 13.8371
Pocillopora_meandrina_HIv1___Sc0000038 2701138 36355023 13.4592 12.239
Pocillopora_meandrina_HIv1___Sc0000039 2599273 32040887 12.3269 11.5546
Pocillopora_meandrina_HIv1___Sc0000040 2445666 35929896 14.6913 14.525
Pocillopora_meandrina_HIv1___Sc0000041 2159376 34045363 15.7663 10.2585
Pocillopora_meandrina_HIv1___Sc0000042 1957488 24529133 12.5309 10.4302
Pocillopora_meandrina_HIv1___Sc0000043 1845599 22370385 12.1209 10.138
Pocillopora_meandrina_HIv1___Sc0000044 1724711 26805366 15.5419 10.4497
Pocillopora_meandrina_HIv1___Sc0000045 1153740 13484750 11.6879 11.3253
Pocillopora_meandrina_HIv1___Sc0000046 755410 7979352 10.5629 15.8232
Pocillopora_meandrina_HIv1___Sc0000047 239089 140790 0.5889 1.9296
Pocillopora_meandrina_HIv1___Sc0000048 214660 48786 0.2273 1.401
Pocillopora_meandrina_HIv1___Sc0000049 179266 491772 2.7433 6.6339
Pocillopora_meandrina_HIv1___Sc0000050 177168 268786 1.5171 4.302
Pocillopora_meandrina_HIv1___Sc0000051 165057 605216 3.6667 6.1436
Pocillopora_meandrina_HIv1___Sc0000052 155210 24508 0.1579 1.8949
Pocillopora_meandrina_HIv1___Sc0000053 123249 147392 1.1959 2.9676
Pocillopora_meandrina_HIv1___Sc0000054 122643 1565519 12.7648 15.7156
Pocillopora_meandrina_HIv1___Sc0000055 121609 688504 5.6616 10.7529
Pocillopora_meandrina_HIv1___Sc0000056 112816 58995 0.5229 5.7153
Pocillopora_meandrina_HIv1___Sc0000057 107171 233320 2.1771 5.3558
Pocillopora_meandrina_HIv1___Sc0000058 98341 29779 0.3028 3.3318
Pocillopora_meandrina_HIv1___Sc0000059 83292 4297 0.0516 0.4245
Pocillopora_meandrina_HIv1___Sc0000060 79483 532 0.0067 0.0822
Pocillopora_meandrina_HIv1___Sc0000061 75390 370583 4.9155 12.0895
Pocillopora_meandrina_HIv1___Sc0000062 74194 14784 0.1993 0.7444
Pocillopora_meandrina_HIv1___Sc0000063 73457 108414 1.4759 12.4402
Pocillopora_meandrina_HIv1___Sc0000064 72700 16092 0.2213 0.9132
Pocillopora_meandrina_HIv1___Sc0000065 67986 10970 0.1614 1.3814
Pocillopora_meandrina_HIv1___Sc0000066 66659 441298 6.6202 7.1103
Pocillopora_meandrina_HIv1___Sc0000067 64947 105672 1.627 3.8297
Pocillopora_meandrina_HIv1___Sc0000068 64340 9674 0.1504 0.9847
Pocillopora_meandrina_HIv1___Sc0000069 62616 171301 2.7357 7.0606
Pocillopora_meandrina_HIv1___Sc0000070 60121 258574 4.3009 26.2016
Pocillopora_meandrina_HIv1___Sc0000071 57157 73090 1.2788 2.579
Pocillopora_meandrina_HIv1___Sc0000072 56626 8740 0.1543 1.7658
Pocillopora_meandrina_HIv1___Sc0000073 56082 16469 0.2937 0.8981
Pocillopora_meandrina_HIv1___Sc0000074 55210 269 0.0049 0.0851
Pocillopora_meandrina_HIv1___Sc0000075 54685 1089 0.0199 0.2351
Pocillopora_meandrina_HIv1___Sc0000076 54587 160822 2.9462 14.5849
Pocillopora_meandrina_HIv1___Sc0000077 53379 19760 0.3702 0.9291
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1353 0.0272 0.2339
Pocillopora_meandrina_HIv1___Sc0000080 47218 60571 1.2828 3.3441
Pocillopora_meandrina_HIv1___Sc0000081 42490 12655 0.2978 1.0032
Pocillopora_meandrina_HIv1___Sc0000082 32657 411554 12.6023 26.7075
Pocillopora_meandrina_HIv1___Sc0000083 27992 3882 0.1387 0.4933
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 7017924 4.3818 7.3816
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3926338 3.2782 5.9926
Pocillopora_meandrina_HIv1___xfSc0000002 779520 9565132 12.2705 17.8032
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2045241 4.4236 8.3371
Pocillopora_meandrina_HIv1___xfSc0000004 334777 644698 1.9258 3.8909
Pocillopora_meandrina_HIv1___xfSc0000006 290100 572146 1.9722 3.9292
Pocillopora_meandrina_HIv1___xfSc0000007 252258 965933 3.8291 6.4284
Pocillopora_meandrina_HIv1___xfSc0000012 148278 774153 5.221 8.3887
Pocillopora_meandrina_HIv1___xfSc0000014 118081 18408 0.1559 0.7787
Pocillopora_meandrina_HIv1___xfSc0000017 98555 383714 3.8934 56.9677
Pocillopora_meandrina_HIv1___xfSc0000021 95778 520946 5.4391 9.6044
Pocillopora_meandrina_HIv1___xfSc0000024 90744 282383 3.1119 5.855
Pocillopora_meandrina_HIv1___xfSc0000029 85532 113727 1.3296 4.7992
Pocillopora_meandrina_HIv1___xfSc0000038 77395 38849 0.502 3.9634
Pocillopora_meandrina_HIv1___xfSc0000058 69718 516961 7.415 9.9959
Pocillopora_meandrina_HIv1___xfSc0000059 69426 297674 4.2876 7.0574
Pocillopora_meandrina_HIv1___xfSc0000074 66573 157851 2.3711 4.059
Pocillopora_meandrina_HIv1___xfSc0000081 65415 493170 7.5391 9.0426
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1188091 18.1896 16.1669
Pocillopora_meandrina_HIv1___xfSc0000092 63607 417238 6.5596 5.5545
Pocillopora_meandrina_HIv1___xfSc0000094 62842 141300 2.2485 4.5307
Pocillopora_meandrina_HIv1___xfSc0000113 60556 851232 14.0569 16.4049
Pocillopora_meandrina_HIv1___xfSc0000132 59032 31668 0.5365 1.502
Pocillopora_meandrina_HIv1___xfSc0000145 58221 265463 4.5596 5.8629
Pocillopora_meandrina_HIv1___xfSc0000146 58151 95504 1.6423 3.6568
Pocillopora_meandrina_HIv1___xfSc0000168 56681 312414 5.5118 8.4695
Pocillopora_meandrina_HIv1___xfSc0000175 56271 208089 3.698 9.458
Pocillopora_meandrina_HIv1___xfSc0000195 55223 12931 0.2342 1.9058
Pocillopora_meandrina_HIv1___xfSc0000199 55095 636800 11.5582 21.6168
Pocillopora_meandrina_HIv1___xfSc0000205 54658 117592 2.1514 4.6471
Pocillopora_meandrina_HIv1___xfSc0000206 54623 225009 4.1193 6.4867
Pocillopora_meandrina_HIv1___xfSc0000212 54299 286489 5.2761 8.6522
Pocillopora_meandrina_HIv1___xfSc0000217 54168 376721 6.9547 14.3396
Pocillopora_meandrina_HIv1___xfSc0000223 53823 305719 5.6801 7.1536
Pocillopora_meandrina_HIv1___xfSc0000228 53382 382227 7.1602 20.9246
Pocillopora_meandrina_HIv1___xfSc0000237 53049 255403 4.8145 6.7642
Pocillopora_meandrina_HIv1___xfSc0000262 52308 411748 7.8716 8.0458
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1388060 26.5586 23.4754
Pocillopora_meandrina_HIv1___xfSc0000272 52107 277689 5.3292 8.1287
Pocillopora_meandrina_HIv1___xfSc0000275 51938 632796 12.1837 15.2335
Pocillopora_meandrina_HIv1___xfSc0000284 51483 593378 11.5257 13.792
Pocillopora_meandrina_HIv1___xfSc0000288 51367 194327 3.7831 11.7871
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9287 0.1827 0.6998
Pocillopora_meandrina_HIv1___xfSc0000301 50809 573755 11.2924 9.2115
Pocillopora_meandrina_HIv1___xfSc0000343 49544 183504 3.7039 7.9095
Pocillopora_meandrina_HIv1___xfSc0000376 48519 354268 7.3016 21.6347
Pocillopora_meandrina_HIv1___xfSc0000415 47398 318244 6.7143 7.7257
Pocillopora_meandrina_HIv1___xfSc0000423 47202 40959 0.8677 2.7174
Pocillopora_meandrina_HIv1___xfSc0000426 47096 970150 20.5994 25.1012
Pocillopora_meandrina_HIv1___xfSc0000428 47057 250950 5.3329 9.1628
Pocillopora_meandrina_HIv1___xfSc0000436 46816 276637 5.909 10.2864
Pocillopora_meandrina_HIv1___xfSc0000445 46561 40073 0.8607 2.294
Pocillopora_meandrina_HIv1___xfSc0000447 46542 384950 8.271 10.4817
Pocillopora_meandrina_HIv1___xfSc0000469 45938 297370 6.4733 6.9986
Pocillopora_meandrina_HIv1___xfSc0000477 45781 277312 6.0574 6.3567
Pocillopora_meandrina_HIv1___xfSc0000479 45736 164418 3.5949 5.7973
Pocillopora_meandrina_HIv1___xfSc0000482 45585 265557 5.8255 10.3259
Pocillopora_meandrina_HIv1___xfSc0000488 45379 159799 3.5214 5.7393
Pocillopora_meandrina_HIv1___xfSc0000506 44781 182575 4.0771 6.2506
Pocillopora_meandrina_HIv1___xfSc0000527 44235 225401 5.0955 7.4737
Pocillopora_meandrina_HIv1___xfSc0000540 43935 346845 7.8945 10.8203
Pocillopora_meandrina_HIv1___xfSc0000555 43535 233671 5.3674 9.5312
Pocillopora_meandrina_HIv1___xfSc0000565 43357 276255 6.3716 6.0035
Pocillopora_meandrina_HIv1___xfSc0000566 43316 177583 4.0997 6.4033
Pocillopora_meandrina_HIv1___xfSc0000567 43305 140757 3.2504 6.4527
Pocillopora_meandrina_HIv1___xfSc0000570 43295 152839 3.5302 9.1416
Pocillopora_meandrina_HIv1___xfSc0000579 43029 99324 2.3083 5.0244
Pocillopora_meandrina_HIv1___xfSc0000583 42958 297293 6.9206 7.9749
Pocillopora_meandrina_HIv1___xfSc0000596 42675 207486 4.862 7.778
Pocillopora_meandrina_HIv1___xfSc0000612 42423 104477 2.4627 4.631
Pocillopora_meandrina_HIv1___xfSc0000616 42355 4916731 116.0838 365.4527
Pocillopora_meandrina_HIv1___xfSc0000621 42164 294910 6.9944 8.3962
Pocillopora_meandrina_HIv1___xfSc0000642 41754 150143 3.5959 6.533
Pocillopora_meandrina_HIv1___xfSc0000655 41446 335257 8.089 15.1512
Pocillopora_meandrina_HIv1___xfSc0000692 40426 245183 6.065 7.4463
Pocillopora_meandrina_HIv1___xfSc0000699 40296 29257 0.7261 2.0008
Pocillopora_meandrina_HIv1___xfSc0000704 40233 361017 8.9732 11.7709
Pocillopora_meandrina_HIv1___xfSc0000705 40197 121857 3.0315 5.6087
Pocillopora_meandrina_HIv1___xfSc0000716 39998 262148 6.554 7.7279
Pocillopora_meandrina_HIv1___xfSc0000725 39827 66951 1.681 5.0009
Pocillopora_meandrina_HIv1___xfSc0000729 39775 41116 1.0337 7.358
Pocillopora_meandrina_HIv1___xfSc0000760 39228 12029 0.3066 1.3296
Pocillopora_meandrina_HIv1___xfSc0000763 39151 237090 6.0558 6.8587
Pocillopora_meandrina_HIv1___xfSc0000765 39117 88295 2.2572 5.226
Pocillopora_meandrina_HIv1___xfSc0000788 38513 375981 9.7624 12.0615
Pocillopora_meandrina_HIv1___xfSc0000811 37888 304135 8.0272 7.794
Pocillopora_meandrina_HIv1___xfSc0000812 37881 29158 0.7697 1.5891
Pocillopora_meandrina_HIv1___xfSc0000817 37779 298188 7.893 6.7488
Pocillopora_meandrina_HIv1___xfSc0000824 37656 222907 5.9196 9.5484
Pocillopora_meandrina_HIv1___xfSc0000835 37434 118525 3.1662 5.0526
Pocillopora_meandrina_HIv1___xfSc0000836 37372 235697 6.3068 9.0386
Pocillopora_meandrina_HIv1___xfSc0000837 37368 399781 10.6985 9.7635
Pocillopora_meandrina_HIv1___xfSc0000840 37283 219278 5.8814 13.5902
Pocillopora_meandrina_HIv1___xfSc0000857 37006 143344 3.8735 5.143
Pocillopora_meandrina_HIv1___xfSc0000859 36995 30538 0.8255 1.6189
Pocillopora_meandrina_HIv1___xfSc0000866 36925 27476 0.7441 1.5467
Pocillopora_meandrina_HIv1___xfSc0000868 36831 92076 2.5 5.5108
Pocillopora_meandrina_HIv1___xfSc0000875 36611 25933 0.7083 1.7374
Pocillopora_meandrina_HIv1___xfSc0000885 36416 167879 4.61 6.4261
Pocillopora_meandrina_HIv1___xfSc0000886 36355 94909 2.6106 4.0878
Pocillopora_meandrina_HIv1___xfSc0000890 36339 179107 4.9288 11.4104
Pocillopora_meandrina_HIv1___xfSc0000892 36267 120284 3.3166 20.9885
Pocillopora_meandrina_HIv1___xfSc0000943 35168 6736 0.1915 0.6694
Pocillopora_meandrina_HIv1___xfSc0000948 35100 200066 5.6999 7.6261
Pocillopora_meandrina_HIv1___xfSc0000952 34934 375186 10.7399 7.6996
Pocillopora_meandrina_HIv1___xfSc0000953 34905 152243 4.3616 6.079
Pocillopora_meandrina_HIv1___xfSc0000957 34773 154392 4.44 7.565
Pocillopora_meandrina_HIv1___xfSc0000968 34345 11438 0.333 1.2639
Pocillopora_meandrina_HIv1___xfSc0000974 34140 256627 7.5169 9.5784
Pocillopora_meandrina_HIv1___xfSc0000975 33988 237298 6.9818 6.9083
Pocillopora_meandrina_HIv1___xfSc0000995 33324 86874 2.6069 6.1022
Pocillopora_meandrina_HIv1___xfSc0001011 32918 132533 4.0262 6.5263
Pocillopora_meandrina_HIv1___xfSc0001122 29140 260560 8.9417 7.9509
Pocillopora_meandrina_HIv1___xfSc0001170 27381 18362 0.6706 1.7329
Pocillopora_meandrina_HIv1___xfSc0001179 27200 85319 3.1367 5.3017
Pocillopora_meandrina_HIv1___xfSc0001231 22938 17761 0.7743 1.3398
Pocillopora_meandrina_HIv1___xfSc0001237 22715 94928 4.1791 11.3182
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2043604 5.0055 8.2261
Pocillopora_meandrina_HIv1___xpSc0001275 48561 176236 3.6292 7.0225
Pocillopora_meandrina_HIv1___xpSc0001276 38618 71883 1.8614 6.0559
Pocillopora_meandrina_HIv1___xpSc0001280 35955 116676 3.2451 4.6165
Pocillopora_meandrina_HIv1___xpSc0001281 34238 158951 4.6425 7.4297
Pocillopora_meandrina_HIv1___xpSc0001290 28931 128399 4.4381 5.6497
Pocillopora_meandrina_HIv1___xpSc0001321 15304 49896 3.2603 6.6874
Pocillopora_meandrina_HIv1___xpSc0001331 8958 127702 14.2556 9.3435
Pocillopora_meandrina_HIv1___xpSc0001337 6786 75123 11.0703 5.9728
Pocillopora_meandrina_HIv1___xpSc0001344 5647 53867 9.539 12.2094
Pocillopora_meandrina_HIv1___xpSc0001355 3576 44410 12.4189 9.0491

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 21:06:38
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