Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-255-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-255-TP2_R1_001.fastp-trim.fq.gz -2 POC-255-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-255-TP2 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:27:59 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-255-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 47,096,040
Mapped reads 47,096,040 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 47,096,040 / 100%
Mapped reads, first in pair 23,548,020 / 50%
Mapped reads, second in pair 23,548,020 / 50%
Mapped reads, both in pair 47,096,040 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 130.71
Overlapping read pairs 16,441,958 / 69.82%
Duplicated reads (estimated) 6,251,806 / 13.27%
Duplication rate 12.58%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,468,428,387 / 40.28%
Number/percentage of C's 600,054,542 / 9.79%
Number/percentage of T's 2,470,237,515 / 40.31%
Number/percentage of G's 589,439,903 / 9.62%
Number/percentage of N's 519,821 / 0.01%
GC Percentage 19.41%

Coverage

Mean 16.3265
Standard Deviation 15.5433
Mean (paired-end reads overlap ignored) 13.25

Mapping Quality

Mean Mapping Quality 22.6

Insert size

Mean 230.57
Standard Deviation 82.1
P25/Median/P75 165 / 224 / 282

Mismatches and indels

General error rate 20.99%
Mismatches 1,263,517,992
Insertions 9,110,873
Mapped reads with at least one insertion 14.55%
Deletions 7,273,258
Mapped reads with at least one deletion 12.98%
Homopolymer indels 52.25%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 389578090 17.9934 13.6108
Pocillopora_meandrina_HIv1___Sc0000001 21507942 395479486 18.3876 12.4624
Pocillopora_meandrina_HIv1___Sc0000002 19741974 363145922 18.3946 12.9542
Pocillopora_meandrina_HIv1___Sc0000003 19417450 312307300 16.0838 14.1234
Pocillopora_meandrina_HIv1___Sc0000004 14584444 231326161 15.8612 20.5835
Pocillopora_meandrina_HIv1___Sc0000005 14098929 244575030 17.3471 12.2413
Pocillopora_meandrina_HIv1___Sc0000006 14068054 244479292 17.3783 13.048
Pocillopora_meandrina_HIv1___Sc0000007 13590779 233243440 17.1619 13.7473
Pocillopora_meandrina_HIv1___Sc0000008 12446599 228537469 18.3614 13.0406
Pocillopora_meandrina_HIv1___Sc0000009 11983232 117450472 9.8012 15.316
Pocillopora_meandrina_HIv1___Sc0000010 11763137 192086973 16.3296 16.6833
Pocillopora_meandrina_HIv1___Sc0000011 10501528 209302646 19.9307 11.178
Pocillopora_meandrina_HIv1___Sc0000012 10024633 168467863 16.8054 17.6726
Pocillopora_meandrina_HIv1___Sc0000013 9946974 122880401 12.3535 12.8163
Pocillopora_meandrina_HIv1___Sc0000014 9536826 176799460 18.5386 12.6997
Pocillopora_meandrina_HIv1___Sc0000015 9393205 156514836 16.6626 12.3227
Pocillopora_meandrina_HIv1___Sc0000016 9288165 155304427 16.7207 13.5076
Pocillopora_meandrina_HIv1___Sc0000017 9274345 159053829 17.1499 12.7945
Pocillopora_meandrina_HIv1___Sc0000018 8584156 153698338 17.9049 12.7247
Pocillopora_meandrina_HIv1___Sc0000019 7112774 123402538 17.3494 14.1734
Pocillopora_meandrina_HIv1___Sc0000020 6748058 118593203 17.5744 15.1582
Pocillopora_meandrina_HIv1___Sc0000021 6546105 118675823 18.1292 12.6539
Pocillopora_meandrina_HIv1___Sc0000022 6319256 101920207 16.1285 18.0762
Pocillopora_meandrina_HIv1___Sc0000023 5767069 85769902 14.8724 14.1769
Pocillopora_meandrina_HIv1___Sc0000024 5762297 66472258 11.5357 14.1465
Pocillopora_meandrina_HIv1___Sc0000025 5759531 80755777 14.0212 13.8987
Pocillopora_meandrina_HIv1___Sc0000026 5647578 113920910 20.1716 12.3361
Pocillopora_meandrina_HIv1___Sc0000027 5550630 76645843 13.8085 14.7334
Pocillopora_meandrina_HIv1___Sc0000028 5130920 97217565 18.9474 14.6056
Pocillopora_meandrina_HIv1___Sc0000029 4860867 75914207 15.6174 12.3979
Pocillopora_meandrina_HIv1___Sc0000030 4843735 86880849 17.9367 11.4378
Pocillopora_meandrina_HIv1___Sc0000031 4691590 83165120 17.7264 14.0813
Pocillopora_meandrina_HIv1___Sc0000032 3615800 65910556 18.2285 12.3975
Pocillopora_meandrina_HIv1___Sc0000033 3306609 44217238 13.3724 13.2636
Pocillopora_meandrina_HIv1___Sc0000034 3122802 56282150 18.023 13.011
Pocillopora_meandrina_HIv1___Sc0000035 3015365 40052116 13.2827 14.1491
Pocillopora_meandrina_HIv1___Sc0000036 3007169 57756761 19.2064 11.2009
Pocillopora_meandrina_HIv1___Sc0000037 2860435 48121866 16.8233 19.1427
Pocillopora_meandrina_HIv1___Sc0000038 2701138 43266301 16.0178 13.6614
Pocillopora_meandrina_HIv1___Sc0000039 2599273 34117948 13.126 15.7748
Pocillopora_meandrina_HIv1___Sc0000040 2445666 44849820 18.3385 19.1579
Pocillopora_meandrina_HIv1___Sc0000041 2159376 41549601 19.2415 12.4742
Pocillopora_meandrina_HIv1___Sc0000042 1957488 27698643 14.1501 12.8469
Pocillopora_meandrina_HIv1___Sc0000043 1845599 26619849 14.4234 12.2671
Pocillopora_meandrina_HIv1___Sc0000044 1724711 30218124 17.5207 15.2786
Pocillopora_meandrina_HIv1___Sc0000045 1153740 17430201 15.1076 13.5439
Pocillopora_meandrina_HIv1___Sc0000046 755410 8420981 11.1476 15.8246
Pocillopora_meandrina_HIv1___Sc0000047 239089 433683 1.8139 5.2303
Pocillopora_meandrina_HIv1___Sc0000048 214660 50237 0.234 1.5107
Pocillopora_meandrina_HIv1___Sc0000049 179266 693352 3.8677 7.2197
Pocillopora_meandrina_HIv1___Sc0000050 177168 193632 1.0929 3.3799
Pocillopora_meandrina_HIv1___Sc0000051 165057 828715 5.0208 9.0249
Pocillopora_meandrina_HIv1___Sc0000052 155210 138774 0.8941 10.2748
Pocillopora_meandrina_HIv1___Sc0000053 123249 390455 3.168 7.2184
Pocillopora_meandrina_HIv1___Sc0000054 122643 1627694 13.2718 14.5163
Pocillopora_meandrina_HIv1___Sc0000055 121609 631981 5.1968 12.4094
Pocillopora_meandrina_HIv1___Sc0000056 112816 65305 0.5789 4.9075
Pocillopora_meandrina_HIv1___Sc0000057 107171 286270 2.6712 6.8479
Pocillopora_meandrina_HIv1___Sc0000058 98341 78816 0.8015 7.4998
Pocillopora_meandrina_HIv1___Sc0000059 83292 3412 0.041 0.2848
Pocillopora_meandrina_HIv1___Sc0000060 79483 781 0.0098 0.1878
Pocillopora_meandrina_HIv1___Sc0000061 75390 212920 2.8242 6.8058
Pocillopora_meandrina_HIv1___Sc0000062 74194 22405 0.302 1.4663
Pocillopora_meandrina_HIv1___Sc0000063 73457 27479 0.3741 3.7055
Pocillopora_meandrina_HIv1___Sc0000064 72700 3740 0.0514 0.2693
Pocillopora_meandrina_HIv1___Sc0000065 67986 2511 0.0369 0.3279
Pocillopora_meandrina_HIv1___Sc0000066 66659 476346 7.146 7.7606
Pocillopora_meandrina_HIv1___Sc0000067 64947 118303 1.8215 3.9355
Pocillopora_meandrina_HIv1___Sc0000068 64340 8256 0.1283 0.8351
Pocillopora_meandrina_HIv1___Sc0000069 62616 189916 3.033 7.6599
Pocillopora_meandrina_HIv1___Sc0000070 60121 316478 5.264 29.0874
Pocillopora_meandrina_HIv1___Sc0000071 57157 67285 1.1772 2.4487
Pocillopora_meandrina_HIv1___Sc0000072 56626 12885 0.2275 2.534
Pocillopora_meandrina_HIv1___Sc0000073 56082 9125 0.1627 0.6001
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 1072 0.0196 0.2172
Pocillopora_meandrina_HIv1___Sc0000076 54587 230680 4.2259 21.0741
Pocillopora_meandrina_HIv1___Sc0000077 53379 17266 0.3235 0.8358
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1075 0.0216 0.2131
Pocillopora_meandrina_HIv1___Sc0000080 47218 93411 1.9783 4.8674
Pocillopora_meandrina_HIv1___Sc0000081 42490 23799 0.5601 2.0095
Pocillopora_meandrina_HIv1___Sc0000082 32657 561613 17.1973 40.194
Pocillopora_meandrina_HIv1___Sc0000083 27992 2658 0.095 0.531
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 12122645 7.569 13.4039
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4919929 4.1078 9.0179
Pocillopora_meandrina_HIv1___xfSc0000002 779520 7220445 9.2627 13.0911
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1383663 2.9927 6.3114
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1072968 3.205 6.3931
Pocillopora_meandrina_HIv1___xfSc0000006 290100 520256 1.7934 4.2065
Pocillopora_meandrina_HIv1___xfSc0000007 252258 697165 2.7637 5.4608
Pocillopora_meandrina_HIv1___xfSc0000012 148278 477361 3.2194 6.3726
Pocillopora_meandrina_HIv1___xfSc0000014 118081 26736 0.2264 0.9387
Pocillopora_meandrina_HIv1___xfSc0000017 98555 432397 4.3874 68.6253
Pocillopora_meandrina_HIv1___xfSc0000021 95778 423922 4.4261 8.8076
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1101318 12.1365 16.0529
Pocillopora_meandrina_HIv1___xfSc0000029 85532 179424 2.0977 5.4042
Pocillopora_meandrina_HIv1___xfSc0000038 77395 23581 0.3047 2.7222
Pocillopora_meandrina_HIv1___xfSc0000058 69718 834965 11.9763 12.3377
Pocillopora_meandrina_HIv1___xfSc0000059 69426 466959 6.726 10.8064
Pocillopora_meandrina_HIv1___xfSc0000074 66573 257265 3.8644 6.7036
Pocillopora_meandrina_HIv1___xfSc0000081 65415 254945 3.8973 6.5458
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1010874 15.4764 16.3474
Pocillopora_meandrina_HIv1___xfSc0000092 63607 608428 9.5654 10.4608
Pocillopora_meandrina_HIv1___xfSc0000094 62842 151325 2.408 5.4924
Pocillopora_meandrina_HIv1___xfSc0000113 60556 867847 14.3313 16.1518
Pocillopora_meandrina_HIv1___xfSc0000132 59032 39390 0.6673 1.8943
Pocillopora_meandrina_HIv1___xfSc0000145 58221 375511 6.4498 6.682
Pocillopora_meandrina_HIv1___xfSc0000146 58151 200035 3.4399 8.2227
Pocillopora_meandrina_HIv1___xfSc0000168 56681 333643 5.8863 9.2158
Pocillopora_meandrina_HIv1___xfSc0000175 56271 225699 4.0109 11.793
Pocillopora_meandrina_HIv1___xfSc0000195 55223 4795 0.0868 0.7973
Pocillopora_meandrina_HIv1___xfSc0000199 55095 297755 5.4044 10.7589
Pocillopora_meandrina_HIv1___xfSc0000205 54658 334316 6.1165 13.4966
Pocillopora_meandrina_HIv1___xfSc0000206 54623 211796 3.8774 6.3803
Pocillopora_meandrina_HIv1___xfSc0000212 54299 329649 6.071 9.8105
Pocillopora_meandrina_HIv1___xfSc0000217 54168 302826 5.5905 11.6842
Pocillopora_meandrina_HIv1___xfSc0000223 53823 292412 5.4328 7.5164
Pocillopora_meandrina_HIv1___xfSc0000228 53382 504248 9.446 26.4883
Pocillopora_meandrina_HIv1___xfSc0000237 53049 261624 4.9317 7.7413
Pocillopora_meandrina_HIv1___xfSc0000262 52308 204634 3.9121 5.7136
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1711130 32.7401 29.5685
Pocillopora_meandrina_HIv1___xfSc0000272 52107 389287 7.4709 9.5096
Pocillopora_meandrina_HIv1___xfSc0000275 51938 388183 7.474 10.6072
Pocillopora_meandrina_HIv1___xfSc0000284 51483 570086 11.0733 14.6304
Pocillopora_meandrina_HIv1___xfSc0000288 51367 687495 13.384 11.7466
Pocillopora_meandrina_HIv1___xfSc0000300 50845 7507 0.1476 0.7971
Pocillopora_meandrina_HIv1___xfSc0000301 50809 491301 9.6696 12.4568
Pocillopora_meandrina_HIv1___xfSc0000343 49544 140608 2.838 5.0662
Pocillopora_meandrina_HIv1___xfSc0000376 48519 364911 7.521 21.3925
Pocillopora_meandrina_HIv1___xfSc0000415 47398 209328 4.4164 5.8551
Pocillopora_meandrina_HIv1___xfSc0000423 47202 51846 1.0984 2.7535
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1688579 35.854 36.5032
Pocillopora_meandrina_HIv1___xfSc0000428 47057 372767 7.9216 14.7274
Pocillopora_meandrina_HIv1___xfSc0000436 46816 318159 6.7959 10.5796
Pocillopora_meandrina_HIv1___xfSc0000445 46561 64042 1.3754 3.9956
Pocillopora_meandrina_HIv1___xfSc0000447 46542 214954 4.6185 7.1944
Pocillopora_meandrina_HIv1___xfSc0000469 45938 436662 9.5055 9.7689
Pocillopora_meandrina_HIv1___xfSc0000477 45781 184792 4.0364 6.0363
Pocillopora_meandrina_HIv1___xfSc0000479 45736 178312 3.8987 6.2759
Pocillopora_meandrina_HIv1___xfSc0000482 45585 665897 14.6078 22.4709
Pocillopora_meandrina_HIv1___xfSc0000488 45379 239335 5.2741 8.9505
Pocillopora_meandrina_HIv1___xfSc0000506 44781 130756 2.9199 4.9097
Pocillopora_meandrina_HIv1___xfSc0000527 44235 219793 4.9688 7.3037
Pocillopora_meandrina_HIv1___xfSc0000540 43935 353395 8.0436 9.6705
Pocillopora_meandrina_HIv1___xfSc0000555 43535 184326 4.234 8.5594
Pocillopora_meandrina_HIv1___xfSc0000565 43357 573130 13.2189 11.7707
Pocillopora_meandrina_HIv1___xfSc0000566 43316 238615 5.5087 8.092
Pocillopora_meandrina_HIv1___xfSc0000567 43305 192618 4.4479 8.9217
Pocillopora_meandrina_HIv1___xfSc0000570 43295 73738 1.7032 4.5705
Pocillopora_meandrina_HIv1___xfSc0000579 43029 84796 1.9707 4.9108
Pocillopora_meandrina_HIv1___xfSc0000583 42958 339068 7.893 8.8077
Pocillopora_meandrina_HIv1___xfSc0000596 42675 304795 7.1422 11.9432
Pocillopora_meandrina_HIv1___xfSc0000612 42423 123140 2.9027 5.1237
Pocillopora_meandrina_HIv1___xfSc0000616 42355 6808779 160.755 535.452
Pocillopora_meandrina_HIv1___xfSc0000621 42164 502163 11.9098 13.9621
Pocillopora_meandrina_HIv1___xfSc0000642 41754 372609 8.9239 11.6892
Pocillopora_meandrina_HIv1___xfSc0000655 41446 175271 4.2289 9.4618
Pocillopora_meandrina_HIv1___xfSc0000692 40426 144226 3.5677 6.102
Pocillopora_meandrina_HIv1___xfSc0000699 40296 13830 0.3432 1.0205
Pocillopora_meandrina_HIv1___xfSc0000704 40233 543127 13.4995 18.709
Pocillopora_meandrina_HIv1___xfSc0000705 40197 137297 3.4156 6.78
Pocillopora_meandrina_HIv1___xfSc0000716 39998 260523 6.5134 7.3385
Pocillopora_meandrina_HIv1___xfSc0000725 39827 101994 2.5609 8.7616
Pocillopora_meandrina_HIv1___xfSc0000729 39775 14853 0.3734 2.4948
Pocillopora_meandrina_HIv1___xfSc0000760 39228 8551 0.218 1.2401
Pocillopora_meandrina_HIv1___xfSc0000763 39151 230743 5.8937 6.4369
Pocillopora_meandrina_HIv1___xfSc0000765 39117 78019 1.9945 4.5733
Pocillopora_meandrina_HIv1___xfSc0000788 38513 515512 13.3854 16.6604
Pocillopora_meandrina_HIv1___xfSc0000811 37888 396694 10.4702 10.7614
Pocillopora_meandrina_HIv1___xfSc0000812 37881 17521 0.4625 1.0122
Pocillopora_meandrina_HIv1___xfSc0000817 37779 461752 12.2225 10.0984
Pocillopora_meandrina_HIv1___xfSc0000824 37656 108001 2.8681 5.3029
Pocillopora_meandrina_HIv1___xfSc0000835 37434 151551 4.0485 7.1358
Pocillopora_meandrina_HIv1___xfSc0000836 37372 232722 6.2272 9.5395
Pocillopora_meandrina_HIv1___xfSc0000837 37368 434124 11.6175 8.812
Pocillopora_meandrina_HIv1___xfSc0000840 37283 259208 6.9524 10.0653
Pocillopora_meandrina_HIv1___xfSc0000857 37006 112758 3.047 5.4775
Pocillopora_meandrina_HIv1___xfSc0000859 36995 54079 1.4618 3.1183
Pocillopora_meandrina_HIv1___xfSc0000866 36925 60480 1.6379 4.6906
Pocillopora_meandrina_HIv1___xfSc0000868 36831 113968 3.0943 9.8119
Pocillopora_meandrina_HIv1___xfSc0000875 36611 129944 3.5493 9.1169
Pocillopora_meandrina_HIv1___xfSc0000885 36416 155445 4.2686 6.4662
Pocillopora_meandrina_HIv1___xfSc0000886 36355 225999 6.2164 11.4513
Pocillopora_meandrina_HIv1___xfSc0000890 36339 217736 5.9918 8.2947
Pocillopora_meandrina_HIv1___xfSc0000892 36267 267653 7.3801 39.7584
Pocillopora_meandrina_HIv1___xfSc0000943 35168 7492 0.213 0.8964
Pocillopora_meandrina_HIv1___xfSc0000948 35100 229544 6.5397 8.5499
Pocillopora_meandrina_HIv1___xfSc0000952 34934 106114 3.0376 6.556
Pocillopora_meandrina_HIv1___xfSc0000953 34905 156101 4.4722 5.845
Pocillopora_meandrina_HIv1___xfSc0000957 34773 149546 4.3006 8.1358
Pocillopora_meandrina_HIv1___xfSc0000968 34345 16075 0.468 1.7347
Pocillopora_meandrina_HIv1___xfSc0000974 34140 265432 7.7748 8.9375
Pocillopora_meandrina_HIv1___xfSc0000975 33988 371569 10.9324 10.6538
Pocillopora_meandrina_HIv1___xfSc0000995 33324 75555 2.2673 5.708
Pocillopora_meandrina_HIv1___xfSc0001011 32918 166056 5.0445 8.6782
Pocillopora_meandrina_HIv1___xfSc0001122 29140 190608 6.5411 7.3454
Pocillopora_meandrina_HIv1___xfSc0001170 27381 19242 0.7028 1.852
Pocillopora_meandrina_HIv1___xfSc0001179 27200 91455 3.3623 6.5452
Pocillopora_meandrina_HIv1___xfSc0001231 22938 17440 0.7603 1.6292
Pocillopora_meandrina_HIv1___xfSc0001237 22715 98998 4.3583 12.3873
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2568913 6.2922 12.9498
Pocillopora_meandrina_HIv1___xpSc0001275 48561 249669 5.1413 11.1928
Pocillopora_meandrina_HIv1___xpSc0001276 38618 95678 2.4775 5.4926
Pocillopora_meandrina_HIv1___xpSc0001280 35955 187272 5.2085 7.7277
Pocillopora_meandrina_HIv1___xpSc0001281 34238 220027 6.4264 10.5684
Pocillopora_meandrina_HIv1___xpSc0001290 28931 212743 7.3535 8.1742
Pocillopora_meandrina_HIv1___xpSc0001321 15304 62236 4.0666 7.0203
Pocillopora_meandrina_HIv1___xpSc0001331 8958 190094 21.2206 11.1468
Pocillopora_meandrina_HIv1___xpSc0001337 6786 11301 1.6653 3.7016
Pocillopora_meandrina_HIv1___xpSc0001344 5647 48516 8.5915 11.9823
Pocillopora_meandrina_HIv1___xpSc0001355 3576 36189 10.12 8.4883

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 21:28:02
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