Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-201-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-201-TP1_R1_001.fastp-trim.fq.gz -2 POC-201-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-201-TP1 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 00:16:59 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-201-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 48,024,220
Mapped reads 48,024,220 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 48,024,220 / 100%
Mapped reads, first in pair 24,012,110 / 50%
Mapped reads, second in pair 24,012,110 / 50%
Mapped reads, both in pair 48,024,220 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.21
Overlapping read pairs 12,953,202 / 53.94%
Duplicated reads (estimated) 5,586,855 / 11.63%
Duplication rate 11.3%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,572,019,144 / 40.38%
Number/percentage of C's 617,820,983 / 9.7%
Number/percentage of T's 2,573,388,782 / 40.41%
Number/percentage of G's 605,088,364 / 9.5%
Number/percentage of N's 524,795 / 0.01%
GC Percentage 19.2%

Coverage

Mean 16.9672
Standard Deviation 15.1358
Mean (paired-end reads overlap ignored) 14.8

Mapping Quality

Mean Mapping Quality 22.61

Insert size

Mean 266.77
Standard Deviation 87.59
P25/Median/P75 202 / 260 / 324

Mismatches and indels

General error rate 21.09%
Mismatches 1,318,697,738
Insertions 9,570,016
Mapped reads with at least one insertion 14.97%
Deletions 7,651,212
Mapped reads with at least one deletion 13.35%
Homopolymer indels 52.3%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 407754660 18.8329 13.847
Pocillopora_meandrina_HIv1___Sc0000001 21507942 407873039 18.9638 12.5427
Pocillopora_meandrina_HIv1___Sc0000002 19741974 373052332 18.8964 13.2766
Pocillopora_meandrina_HIv1___Sc0000003 19417450 317374997 16.3448 14.8852
Pocillopora_meandrina_HIv1___Sc0000004 14584444 244888511 16.7911 26.7733
Pocillopora_meandrina_HIv1___Sc0000005 14098929 255594283 18.1286 12.1008
Pocillopora_meandrina_HIv1___Sc0000006 14068054 255115903 18.1344 13.5043
Pocillopora_meandrina_HIv1___Sc0000007 13590779 237520085 17.4766 13.9698
Pocillopora_meandrina_HIv1___Sc0000008 12446599 236859795 19.0301 13.2906
Pocillopora_meandrina_HIv1___Sc0000009 11983232 127809334 10.6657 17.1204
Pocillopora_meandrina_HIv1___Sc0000010 11763137 194410292 16.5271 15.1203
Pocillopora_meandrina_HIv1___Sc0000011 10501528 218899192 20.8445 11.4889
Pocillopora_meandrina_HIv1___Sc0000012 10024633 175464035 17.5033 14.2996
Pocillopora_meandrina_HIv1___Sc0000013 9946974 137790605 13.8525 13.5791
Pocillopora_meandrina_HIv1___Sc0000014 9536826 183687021 19.2608 12.5736
Pocillopora_meandrina_HIv1___Sc0000015 9393205 166192830 17.6929 12.8395
Pocillopora_meandrina_HIv1___Sc0000016 9288165 164211084 17.6796 13.9661
Pocillopora_meandrina_HIv1___Sc0000017 9274345 160920783 17.3512 12.5919
Pocillopora_meandrina_HIv1___Sc0000018 8584156 156591680 18.2419 12.2394
Pocillopora_meandrina_HIv1___Sc0000019 7112774 123250611 17.3281 13.7506
Pocillopora_meandrina_HIv1___Sc0000020 6748058 121499774 18.0051 17.4019
Pocillopora_meandrina_HIv1___Sc0000021 6546105 119477245 18.2517 12.5216
Pocillopora_meandrina_HIv1___Sc0000022 6319256 102892769 16.2824 16.0592
Pocillopora_meandrina_HIv1___Sc0000023 5767069 83438241 14.468 12.7192
Pocillopora_meandrina_HIv1___Sc0000024 5762297 59791425 10.3763 12.4362
Pocillopora_meandrina_HIv1___Sc0000025 5759531 90227509 15.6658 14.8119
Pocillopora_meandrina_HIv1___Sc0000026 5647578 116925166 20.7036 11.1456
Pocillopora_meandrina_HIv1___Sc0000027 5550630 89668695 16.1547 16.9721
Pocillopora_meandrina_HIv1___Sc0000028 5130920 100959013 19.6766 14.0759
Pocillopora_meandrina_HIv1___Sc0000029 4860867 76642331 15.7672 12.6484
Pocillopora_meandrina_HIv1___Sc0000030 4843735 90255366 18.6334 11.6775
Pocillopora_meandrina_HIv1___Sc0000031 4691590 83989994 17.9022 12.387
Pocillopora_meandrina_HIv1___Sc0000032 3615800 72439781 20.0342 14.466
Pocillopora_meandrina_HIv1___Sc0000033 3306609 43467045 13.1455 13.3897
Pocillopora_meandrina_HIv1___Sc0000034 3122802 59553995 19.0707 12.9875
Pocillopora_meandrina_HIv1___Sc0000035 3015365 43185500 14.3218 14.3629
Pocillopora_meandrina_HIv1___Sc0000036 3007169 66119262 21.9872 13.6708
Pocillopora_meandrina_HIv1___Sc0000037 2860435 54020092 18.8853 25.2062
Pocillopora_meandrina_HIv1___Sc0000038 2701138 43030712 15.9306 14.3977
Pocillopora_meandrina_HIv1___Sc0000039 2599273 35367904 13.6068 12.6124
Pocillopora_meandrina_HIv1___Sc0000040 2445666 39686984 16.2275 15.2694
Pocillopora_meandrina_HIv1___Sc0000041 2159376 40813973 18.9008 12.399
Pocillopora_meandrina_HIv1___Sc0000042 1957488 30814381 15.7418 13.0334
Pocillopora_meandrina_HIv1___Sc0000043 1845599 29629155 16.054 12.9002
Pocillopora_meandrina_HIv1___Sc0000044 1724711 31554114 18.2953 13.8367
Pocillopora_meandrina_HIv1___Sc0000045 1153740 18341519 15.8974 12.6344
Pocillopora_meandrina_HIv1___Sc0000046 755410 8804926 11.6558 14.0046
Pocillopora_meandrina_HIv1___Sc0000047 239089 467261 1.9543 5.0364
Pocillopora_meandrina_HIv1___Sc0000048 214660 71109 0.3313 1.9055
Pocillopora_meandrina_HIv1___Sc0000049 179266 1043586 5.8214 12.5553
Pocillopora_meandrina_HIv1___Sc0000050 177168 194275 1.0966 2.7525
Pocillopora_meandrina_HIv1___Sc0000051 165057 1503679 9.1101 13.5039
Pocillopora_meandrina_HIv1___Sc0000052 155210 132119 0.8512 8.9916
Pocillopora_meandrina_HIv1___Sc0000053 123249 394647 3.202 6.8636
Pocillopora_meandrina_HIv1___Sc0000054 122643 1730672 14.1115 14.8957
Pocillopora_meandrina_HIv1___Sc0000055 121609 531500 4.3706 8.604
Pocillopora_meandrina_HIv1___Sc0000056 112816 59041 0.5233 5.0862
Pocillopora_meandrina_HIv1___Sc0000057 107171 449697 4.1961 10.4948
Pocillopora_meandrina_HIv1___Sc0000058 98341 75619 0.7689 5.9009
Pocillopora_meandrina_HIv1___Sc0000059 83292 44558 0.535 7.0079
Pocillopora_meandrina_HIv1___Sc0000060 79483 536 0.0067 0.1363
Pocillopora_meandrina_HIv1___Sc0000061 75390 914106 12.125 30.8424
Pocillopora_meandrina_HIv1___Sc0000062 74194 13092 0.1765 0.8503
Pocillopora_meandrina_HIv1___Sc0000063 73457 193837 2.6388 26.3529
Pocillopora_meandrina_HIv1___Sc0000064 72700 22002 0.3026 1.5712
Pocillopora_meandrina_HIv1___Sc0000065 67986 12016 0.1767 1.8012
Pocillopora_meandrina_HIv1___Sc0000066 66659 527307 7.9105 8.4671
Pocillopora_meandrina_HIv1___Sc0000067 64947 109833 1.6911 3.975
Pocillopora_meandrina_HIv1___Sc0000068 64340 7156 0.1112 0.7566
Pocillopora_meandrina_HIv1___Sc0000069 62616 202119 3.2279 8.3494
Pocillopora_meandrina_HIv1___Sc0000070 60121 322815 5.3694 29.332
Pocillopora_meandrina_HIv1___Sc0000071 57157 84837 1.4843 2.9745
Pocillopora_meandrina_HIv1___Sc0000072 56626 19072 0.3368 3.5822
Pocillopora_meandrina_HIv1___Sc0000073 56082 13208 0.2355 0.7414
Pocillopora_meandrina_HIv1___Sc0000074 55210 749 0.0136 0.1565
Pocillopora_meandrina_HIv1___Sc0000075 54685 1619 0.0296 0.2611
Pocillopora_meandrina_HIv1___Sc0000076 54587 187428 3.4336 17.1093
Pocillopora_meandrina_HIv1___Sc0000077 53379 27412 0.5135 1.0576
Pocillopora_meandrina_HIv1___Sc0000078 51564 1591 0.0309 0.2864
Pocillopora_meandrina_HIv1___Sc0000079 49664 270 0.0054 0.0734
Pocillopora_meandrina_HIv1___Sc0000080 47218 98178 2.0792 5.7036
Pocillopora_meandrina_HIv1___Sc0000081 42490 10604 0.2496 0.7432
Pocillopora_meandrina_HIv1___Sc0000082 32657 1419682 43.4725 102.1211
Pocillopora_meandrina_HIv1___Sc0000083 27992 3679 0.1314 0.7308
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 18232877 11.3841 17.728
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5360364 4.4755 8.118
Pocillopora_meandrina_HIv1___xfSc0000002 779520 11741990 15.0631 19.4979
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1853131 4.0081 7.1195
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1042922 3.1153 5.9383
Pocillopora_meandrina_HIv1___xfSc0000006 290100 758185 2.6135 5.0016
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1543508 6.1188 8.503
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1095780 7.39 11.333
Pocillopora_meandrina_HIv1___xfSc0000014 118081 24310 0.2059 0.9433
Pocillopora_meandrina_HIv1___xfSc0000017 98555 846823 8.5924 118.1216
Pocillopora_meandrina_HIv1___xfSc0000021 95778 863063 9.0111 14.555
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1083711 11.9425 15.6587
Pocillopora_meandrina_HIv1___xfSc0000029 85532 217006 2.5371 6.9746
Pocillopora_meandrina_HIv1___xfSc0000038 77395 24373 0.3149 1.6129
Pocillopora_meandrina_HIv1___xfSc0000058 69718 506351 7.2628 11.8549
Pocillopora_meandrina_HIv1___xfSc0000059 69426 226238 3.2587 8.2874
Pocillopora_meandrina_HIv1___xfSc0000074 66573 164367 2.469 4.536
Pocillopora_meandrina_HIv1___xfSc0000081 65415 397922 6.083 7.0216
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1071402 16.4031 18.036
Pocillopora_meandrina_HIv1___xfSc0000092 63607 668818 10.5148 9.6189
Pocillopora_meandrina_HIv1___xfSc0000094 62842 60888 0.9689 2.6254
Pocillopora_meandrina_HIv1___xfSc0000113 60556 945175 15.6083 16.7299
Pocillopora_meandrina_HIv1___xfSc0000132 59032 73332 1.2422 3.2074
Pocillopora_meandrina_HIv1___xfSc0000145 58221 90892 1.5612 4.7733
Pocillopora_meandrina_HIv1___xfSc0000146 58151 149201 2.5658 5.5954
Pocillopora_meandrina_HIv1___xfSc0000168 56681 374610 6.6091 10.1174
Pocillopora_meandrina_HIv1___xfSc0000175 56271 171035 3.0395 8.4193
Pocillopora_meandrina_HIv1___xfSc0000195 55223 11016 0.1995 1.2497
Pocillopora_meandrina_HIv1___xfSc0000199 55095 243964 4.4281 9.1942
Pocillopora_meandrina_HIv1___xfSc0000205 54658 311324 5.6959 9.1039
Pocillopora_meandrina_HIv1___xfSc0000206 54623 248604 4.5513 6.768
Pocillopora_meandrina_HIv1___xfSc0000212 54299 378752 6.9753 9.9841
Pocillopora_meandrina_HIv1___xfSc0000217 54168 561601 10.3678 20.7373
Pocillopora_meandrina_HIv1___xfSc0000223 53823 397207 7.3799 8.1519
Pocillopora_meandrina_HIv1___xfSc0000228 53382 365898 6.8543 23.5411
Pocillopora_meandrina_HIv1___xfSc0000237 53049 307635 5.7991 7.7828
Pocillopora_meandrina_HIv1___xfSc0000262 52308 549605 10.5071 10.3365
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1260606 24.12 21.1976
Pocillopora_meandrina_HIv1___xfSc0000272 52107 336318 6.4544 8.9654
Pocillopora_meandrina_HIv1___xfSc0000275 51938 213002 4.1011 6.4364
Pocillopora_meandrina_HIv1___xfSc0000284 51483 430881 8.3694 11.5599
Pocillopora_meandrina_HIv1___xfSc0000288 51367 269281 5.2423 15.8332
Pocillopora_meandrina_HIv1___xfSc0000300 50845 8767 0.1724 0.5908
Pocillopora_meandrina_HIv1___xfSc0000301 50809 599805 11.8051 13.0174
Pocillopora_meandrina_HIv1___xfSc0000343 49544 302153 6.0987 8.3336
Pocillopora_meandrina_HIv1___xfSc0000376 48519 327499 6.7499 17.4654
Pocillopora_meandrina_HIv1___xfSc0000415 47398 222844 4.7015 6.3859
Pocillopora_meandrina_HIv1___xfSc0000423 47202 53970 1.1434 2.4076
Pocillopora_meandrina_HIv1___xfSc0000426 47096 849005 18.0271 19.6312
Pocillopora_meandrina_HIv1___xfSc0000428 47057 452434 9.6146 14.9301
Pocillopora_meandrina_HIv1___xfSc0000436 46816 391112 8.3542 17.9491
Pocillopora_meandrina_HIv1___xfSc0000445 46561 87237 1.8736 4.2977
Pocillopora_meandrina_HIv1___xfSc0000447 46542 448074 9.6273 11.0837
Pocillopora_meandrina_HIv1___xfSc0000469 45938 393421 8.5642 8.2084
Pocillopora_meandrina_HIv1___xfSc0000477 45781 322881 7.0527 7.4632
Pocillopora_meandrina_HIv1___xfSc0000479 45736 179551 3.9258 6.8136
Pocillopora_meandrina_HIv1___xfSc0000482 45585 878341 19.2682 31.2929
Pocillopora_meandrina_HIv1___xfSc0000488 45379 299874 6.6082 8.1043
Pocillopora_meandrina_HIv1___xfSc0000506 44781 144766 3.2328 5.2277
Pocillopora_meandrina_HIv1___xfSc0000527 44235 242819 5.4893 7.3992
Pocillopora_meandrina_HIv1___xfSc0000540 43935 402736 9.1666 14.6891
Pocillopora_meandrina_HIv1___xfSc0000555 43535 271372 6.2334 15.3129
Pocillopora_meandrina_HIv1___xfSc0000565 43357 312305 7.2031 6.8814
Pocillopora_meandrina_HIv1___xfSc0000566 43316 292693 6.7572 10.7127
Pocillopora_meandrina_HIv1___xfSc0000567 43305 163561 3.777 6.5347
Pocillopora_meandrina_HIv1___xfSc0000570 43295 79324 1.8322 4.9891
Pocillopora_meandrina_HIv1___xfSc0000579 43029 78183 1.817 4.1062
Pocillopora_meandrina_HIv1___xfSc0000583 42958 357371 8.3191 8.995
Pocillopora_meandrina_HIv1___xfSc0000596 42675 287813 6.7443 11.5963
Pocillopora_meandrina_HIv1___xfSc0000612 42423 100970 2.3801 3.8988
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2892241 68.2857 190.7231
Pocillopora_meandrina_HIv1___xfSc0000621 42164 341828 8.1071 9.4305
Pocillopora_meandrina_HIv1___xfSc0000642 41754 200353 4.7984 7.0054
Pocillopora_meandrina_HIv1___xfSc0000655 41446 944309 22.7841 47.162
Pocillopora_meandrina_HIv1___xfSc0000692 40426 234271 5.7951 6.908
Pocillopora_meandrina_HIv1___xfSc0000699 40296 40384 1.0022 2.2584
Pocillopora_meandrina_HIv1___xfSc0000704 40233 456735 11.3522 14.1846
Pocillopora_meandrina_HIv1___xfSc0000705 40197 124086 3.0869 6.1926
Pocillopora_meandrina_HIv1___xfSc0000716 39998 358162 8.9545 9.7801
Pocillopora_meandrina_HIv1___xfSc0000725 39827 90515 2.2727 7.7984
Pocillopora_meandrina_HIv1___xfSc0000729 39775 19827 0.4985 3.2939
Pocillopora_meandrina_HIv1___xfSc0000760 39228 11765 0.2999 1.3268
Pocillopora_meandrina_HIv1___xfSc0000763 39151 288290 7.3635 7.3198
Pocillopora_meandrina_HIv1___xfSc0000765 39117 86322 2.2068 6.5702
Pocillopora_meandrina_HIv1___xfSc0000788 38513 476763 12.3793 22.3782
Pocillopora_meandrina_HIv1___xfSc0000811 37888 203878 5.3811 7.9319
Pocillopora_meandrina_HIv1___xfSc0000812 37881 30787 0.8127 1.5169
Pocillopora_meandrina_HIv1___xfSc0000817 37779 186408 4.9342 5.3066
Pocillopora_meandrina_HIv1___xfSc0000824 37656 188769 5.013 8.1322
Pocillopora_meandrina_HIv1___xfSc0000835 37434 312473 8.3473 9.943
Pocillopora_meandrina_HIv1___xfSc0000836 37372 311959 8.3474 12.7284
Pocillopora_meandrina_HIv1___xfSc0000837 37368 599579 16.0453 18.6365
Pocillopora_meandrina_HIv1___xfSc0000840 37283 431810 11.582 13.1733
Pocillopora_meandrina_HIv1___xfSc0000857 37006 144483 3.9043 4.8195
Pocillopora_meandrina_HIv1___xfSc0000859 36995 85728 2.3173 3.6946
Pocillopora_meandrina_HIv1___xfSc0000866 36925 44844 1.2145 2.6646
Pocillopora_meandrina_HIv1___xfSc0000868 36831 145149 3.9409 7.5339
Pocillopora_meandrina_HIv1___xfSc0000875 36611 39397 1.0761 3.1887
Pocillopora_meandrina_HIv1___xfSc0000885 36416 235559 6.4686 9.6754
Pocillopora_meandrina_HIv1___xfSc0000886 36355 112653 3.0987 7.1718
Pocillopora_meandrina_HIv1___xfSc0000890 36339 218423 6.0107 9.5367
Pocillopora_meandrina_HIv1___xfSc0000892 36267 174608 4.8145 22.2564
Pocillopora_meandrina_HIv1___xfSc0000943 35168 7536 0.2143 0.8903
Pocillopora_meandrina_HIv1___xfSc0000948 35100 249326 7.1033 9.9452
Pocillopora_meandrina_HIv1___xfSc0000952 34934 461726 13.2171 11.3709
Pocillopora_meandrina_HIv1___xfSc0000953 34905 187540 5.3729 6.4491
Pocillopora_meandrina_HIv1___xfSc0000957 34773 142675 4.103 6.905
Pocillopora_meandrina_HIv1___xfSc0000968 34345 15428 0.4492 1.6607
Pocillopora_meandrina_HIv1___xfSc0000974 34140 252290 7.3899 7.5099
Pocillopora_meandrina_HIv1___xfSc0000975 33988 272171 8.0079 7.8928
Pocillopora_meandrina_HIv1___xfSc0000995 33324 139956 4.1999 8.279
Pocillopora_meandrina_HIv1___xfSc0001011 32918 213414 6.4832 15.0727
Pocillopora_meandrina_HIv1___xfSc0001122 29140 271720 9.3246 12.6514
Pocillopora_meandrina_HIv1___xfSc0001170 27381 13219 0.4828 1.3252
Pocillopora_meandrina_HIv1___xfSc0001179 27200 87566 3.2193 5.3147
Pocillopora_meandrina_HIv1___xfSc0001231 22938 15229 0.6639 1.1995
Pocillopora_meandrina_HIv1___xfSc0001237 22715 89434 3.9372 9.9399
Pocillopora_meandrina_HIv1___xpSc0001273 408270 3003430 7.3565 12.2221
Pocillopora_meandrina_HIv1___xpSc0001275 48561 197302 4.063 8.3689
Pocillopora_meandrina_HIv1___xpSc0001276 38618 109162 2.8267 5.5212
Pocillopora_meandrina_HIv1___xpSc0001280 35955 278825 7.7548 10.4632
Pocillopora_meandrina_HIv1___xpSc0001281 34238 187166 5.4666 7.9708
Pocillopora_meandrina_HIv1___xpSc0001290 28931 133811 4.6252 6.8889
Pocillopora_meandrina_HIv1___xpSc0001321 15304 55341 3.6161 5.8128
Pocillopora_meandrina_HIv1___xpSc0001331 8958 188094 20.9973 9.1474
Pocillopora_meandrina_HIv1___xpSc0001337 6786 21745 3.2044 6.6058
Pocillopora_meandrina_HIv1___xpSc0001344 5647 48733 8.6299 10.243
Pocillopora_meandrina_HIv1___xpSc0001355 3576 47886 13.3909 10.4943

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 00:17:01
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