Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-42-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-42-TP4_R1_001.fastp-trim.fq.gz -2 POC-42-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-42-TP4 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:38:16 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-42-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 41,764,666
Mapped reads 41,764,666 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 41,764,666 / 100%
Mapped reads, first in pair 20,882,333 / 50%
Mapped reads, second in pair 20,882,333 / 50%
Mapped reads, both in pair 41,764,666 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.39
Overlapping read pairs 10,574,148 / 50.64%
Duplicated reads (estimated) 3,910,073 / 9.36%
Duplication rate 9.2%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,237,564,947 / 40.36%
Number/percentage of C's 537,841,920 / 9.7%
Number/percentage of T's 2,241,910,462 / 40.43%
Number/percentage of G's 526,746,801 / 9.5%
Number/percentage of N's 429,637 / 0.01%
GC Percentage 19.2%

Coverage

Mean 14.7722
Standard Deviation 12.8279
Mean (paired-end reads overlap ignored) 13.04

Mapping Quality

Mean Mapping Quality 22.37

Insert size

Mean 274.35
Standard Deviation 89.43
P25/Median/P75 208 / 267 / 334

Mismatches and indels

General error rate 21.2%
Mismatches 1,152,904,236
Insertions 8,900,127
Mapped reads with at least one insertion 15.65%
Deletions 6,895,499
Mapped reads with at least one deletion 13.75%
Homopolymer indels 51.81%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 343771358 15.8778 11.6109
Pocillopora_meandrina_HIv1___Sc0000001 21507942 357023877 16.5996 11.0328
Pocillopora_meandrina_HIv1___Sc0000002 19741974 318249890 16.1205 11.1825
Pocillopora_meandrina_HIv1___Sc0000003 19417450 279717934 14.4055 12.4529
Pocillopora_meandrina_HIv1___Sc0000004 14584444 223203276 15.3042 21.7191
Pocillopora_meandrina_HIv1___Sc0000005 14098929 221691496 15.724 10.5547
Pocillopora_meandrina_HIv1___Sc0000006 14068054 216286474 15.3743 11.397
Pocillopora_meandrina_HIv1___Sc0000007 13590779 216809615 15.9527 12.3202
Pocillopora_meandrina_HIv1___Sc0000008 12446599 203651849 16.362 11.6135
Pocillopora_meandrina_HIv1___Sc0000009 11983232 107409326 8.9633 13.3971
Pocillopora_meandrina_HIv1___Sc0000010 11763137 173478794 14.7477 13.8226
Pocillopora_meandrina_HIv1___Sc0000011 10501528 185229920 17.6384 9.8521
Pocillopora_meandrina_HIv1___Sc0000012 10024633 156105253 15.5722 14.3004
Pocillopora_meandrina_HIv1___Sc0000013 9946974 122121488 12.2773 11.3586
Pocillopora_meandrina_HIv1___Sc0000014 9536826 154357523 16.1854 11.0297
Pocillopora_meandrina_HIv1___Sc0000015 9393205 141128232 15.0245 11.1085
Pocillopora_meandrina_HIv1___Sc0000016 9288165 142347662 15.3257 11.7523
Pocillopora_meandrina_HIv1___Sc0000017 9274345 140250573 15.1224 10.9756
Pocillopora_meandrina_HIv1___Sc0000018 8584156 134853361 15.7096 10.9002
Pocillopora_meandrina_HIv1___Sc0000019 7112774 106778310 15.0122 12.2134
Pocillopora_meandrina_HIv1___Sc0000020 6748058 102236879 15.1506 11.6187
Pocillopora_meandrina_HIv1___Sc0000021 6546105 105319069 16.0888 10.6639
Pocillopora_meandrina_HIv1___Sc0000022 6319256 96457761 15.2641 15.4227
Pocillopora_meandrina_HIv1___Sc0000023 5767069 76021980 13.1821 11.8283
Pocillopora_meandrina_HIv1___Sc0000024 5762297 65167771 11.3093 13.3305
Pocillopora_meandrina_HIv1___Sc0000025 5759531 72087190 12.5162 12.1423
Pocillopora_meandrina_HIv1___Sc0000026 5647578 101572655 17.9852 10.4654
Pocillopora_meandrina_HIv1___Sc0000027 5550630 79746618 14.3671 14.8287
Pocillopora_meandrina_HIv1___Sc0000028 5130920 83530906 16.2799 11.4506
Pocillopora_meandrina_HIv1___Sc0000029 4860867 71537718 14.7171 11.5698
Pocillopora_meandrina_HIv1___Sc0000030 4843735 77224467 15.9432 10.0083
Pocillopora_meandrina_HIv1___Sc0000031 4691590 75469339 16.0861 11.6366
Pocillopora_meandrina_HIv1___Sc0000032 3615800 59690162 16.5081 11.2897
Pocillopora_meandrina_HIv1___Sc0000033 3306609 38110808 11.5256 11.7787
Pocillopora_meandrina_HIv1___Sc0000034 3122802 52035510 16.6631 11.6065
Pocillopora_meandrina_HIv1___Sc0000035 3015365 40065929 13.2873 13.033
Pocillopora_meandrina_HIv1___Sc0000036 3007169 51643471 17.1735 9.6023
Pocillopora_meandrina_HIv1___Sc0000037 2860435 44264730 15.4748 14.5265
Pocillopora_meandrina_HIv1___Sc0000038 2701138 41241450 15.2682 12.4229
Pocillopora_meandrina_HIv1___Sc0000039 2599273 30315088 11.6629 11.4624
Pocillopora_meandrina_HIv1___Sc0000040 2445666 31125077 12.7266 12.405
Pocillopora_meandrina_HIv1___Sc0000041 2159376 34785649 16.1091 10.5917
Pocillopora_meandrina_HIv1___Sc0000042 1957488 26716722 13.6485 10.97
Pocillopora_meandrina_HIv1___Sc0000043 1845599 19223581 10.4159 9.2918
Pocillopora_meandrina_HIv1___Sc0000044 1724711 27612049 16.0097 11.1717
Pocillopora_meandrina_HIv1___Sc0000045 1153740 15353361 13.3075 11.7473
Pocillopora_meandrina_HIv1___Sc0000046 755410 8226676 10.8903 15.6772
Pocillopora_meandrina_HIv1___Sc0000047 239089 3176666 13.2865 16.2535
Pocillopora_meandrina_HIv1___Sc0000048 214660 102693 0.4784 3.1004
Pocillopora_meandrina_HIv1___Sc0000049 179266 510305 2.8466 8.4816
Pocillopora_meandrina_HIv1___Sc0000050 177168 260219 1.4688 3.0782
Pocillopora_meandrina_HIv1___Sc0000051 165057 759277 4.6001 8.3196
Pocillopora_meandrina_HIv1___Sc0000052 155210 44005 0.2835 2.6398
Pocillopora_meandrina_HIv1___Sc0000053 123249 342935 2.7825 6.1695
Pocillopora_meandrina_HIv1___Sc0000054 122643 1837374 14.9815 13.2151
Pocillopora_meandrina_HIv1___Sc0000055 121609 789789 6.4945 12.2263
Pocillopora_meandrina_HIv1___Sc0000056 112816 60676 0.5378 5.2135
Pocillopora_meandrina_HIv1___Sc0000057 107171 341554 3.187 6.3669
Pocillopora_meandrina_HIv1___Sc0000058 98341 47942 0.4875 5.173
Pocillopora_meandrina_HIv1___Sc0000059 83292 9174 0.1101 0.4984
Pocillopora_meandrina_HIv1___Sc0000060 79483 1627 0.0205 0.1723
Pocillopora_meandrina_HIv1___Sc0000061 75390 631572 8.3774 27.3447
Pocillopora_meandrina_HIv1___Sc0000062 74194 9467 0.1276 0.5936
Pocillopora_meandrina_HIv1___Sc0000063 73457 38463 0.5236 4.219
Pocillopora_meandrina_HIv1___Sc0000064 72700 15341 0.211 0.8437
Pocillopora_meandrina_HIv1___Sc0000065 67986 14850 0.2184 1.5311
Pocillopora_meandrina_HIv1___Sc0000066 66659 430397 6.4567 6.6513
Pocillopora_meandrina_HIv1___Sc0000067 64947 161151 2.4813 4.4027
Pocillopora_meandrina_HIv1___Sc0000068 64340 49384 0.7675 2.0291
Pocillopora_meandrina_HIv1___Sc0000069 62616 406674 6.4947 6.8714
Pocillopora_meandrina_HIv1___Sc0000070 60121 49773 0.8279 3.2217
Pocillopora_meandrina_HIv1___Sc0000071 57157 53608 0.9379 1.7301
Pocillopora_meandrina_HIv1___Sc0000072 56626 11866 0.2096 1.8173
Pocillopora_meandrina_HIv1___Sc0000073 56082 13806 0.2462 0.7824
Pocillopora_meandrina_HIv1___Sc0000074 55210 794 0.0144 0.1313
Pocillopora_meandrina_HIv1___Sc0000075 54685 3074 0.0562 0.2763
Pocillopora_meandrina_HIv1___Sc0000076 54587 175171 3.209 15.2609
Pocillopora_meandrina_HIv1___Sc0000077 53379 37115 0.6953 1.4275
Pocillopora_meandrina_HIv1___Sc0000078 51564 497 0.0096 0.1205
Pocillopora_meandrina_HIv1___Sc0000079 49664 4361 0.0878 0.4304
Pocillopora_meandrina_HIv1___Sc0000080 47218 86857 1.8395 4.4361
Pocillopora_meandrina_HIv1___Sc0000081 42490 5144 0.1211 0.4187
Pocillopora_meandrina_HIv1___Sc0000082 32657 967496 29.626 56.319
Pocillopora_meandrina_HIv1___Sc0000083 27992 142881 5.1044 2.7899
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 11539231 7.2048 11.6272
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5588965 4.6663 8.0744
Pocillopora_meandrina_HIv1___xfSc0000002 779520 8581967 11.0093 13.6995
Pocillopora_meandrina_HIv1___xfSc0000003 462347 3588522 7.7615 13.8333
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1322146 3.9493 6.6226
Pocillopora_meandrina_HIv1___xfSc0000006 290100 1020782 3.5187 6.5248
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2294325 9.0952 11.472
Pocillopora_meandrina_HIv1___xfSc0000012 148278 922958 6.2245 7.877
Pocillopora_meandrina_HIv1___xfSc0000014 118081 31672 0.2682 1.0555
Pocillopora_meandrina_HIv1___xfSc0000017 98555 511775 5.1928 72.2461
Pocillopora_meandrina_HIv1___xfSc0000021 95778 641343 6.6961 10.4412
Pocillopora_meandrina_HIv1___xfSc0000024 90744 520794 5.7392 8.0284
Pocillopora_meandrina_HIv1___xfSc0000029 85532 122343 1.4304 4.9443
Pocillopora_meandrina_HIv1___xfSc0000038 77395 42809 0.5531 5.8717
Pocillopora_meandrina_HIv1___xfSc0000058 69718 724373 10.39 14.7954
Pocillopora_meandrina_HIv1___xfSc0000059 69426 785854 11.3193 13.4116
Pocillopora_meandrina_HIv1___xfSc0000074 66573 682514 10.2521 8.77
Pocillopora_meandrina_HIv1___xfSc0000081 65415 444375 6.7932 6.4801
Pocillopora_meandrina_HIv1___xfSc0000083 65317 801148 12.2655 9.7791
Pocillopora_meandrina_HIv1___xfSc0000092 63607 333921 5.2498 9.3307
Pocillopora_meandrina_HIv1___xfSc0000094 62842 241100 3.8366 6.9035
Pocillopora_meandrina_HIv1___xfSc0000113 60556 892622 14.7404 13.0217
Pocillopora_meandrina_HIv1___xfSc0000132 59032 572288 9.6945 14.6857
Pocillopora_meandrina_HIv1___xfSc0000145 58221 260445 4.4734 5.1094
Pocillopora_meandrina_HIv1___xfSc0000146 58151 511315 8.7929 11.7186
Pocillopora_meandrina_HIv1___xfSc0000168 56681 402868 7.1076 9.3194
Pocillopora_meandrina_HIv1___xfSc0000175 56271 310732 5.5221 12.4921
Pocillopora_meandrina_HIv1___xfSc0000195 55223 166808 3.0206 5.1719
Pocillopora_meandrina_HIv1___xfSc0000199 55095 405093 7.3526 10.4442
Pocillopora_meandrina_HIv1___xfSc0000205 54658 864340 15.8136 14.7744
Pocillopora_meandrina_HIv1___xfSc0000206 54623 339962 6.2238 9.7934
Pocillopora_meandrina_HIv1___xfSc0000212 54299 325404 5.9928 9.1293
Pocillopora_meandrina_HIv1___xfSc0000217 54168 506652 9.3533 14.3719
Pocillopora_meandrina_HIv1___xfSc0000223 53823 334232 6.2098 7.5075
Pocillopora_meandrina_HIv1___xfSc0000228 53382 483322 9.054 21.6424
Pocillopora_meandrina_HIv1___xfSc0000237 53049 441891 8.3299 7.9251
Pocillopora_meandrina_HIv1___xfSc0000262 52308 335268 6.4095 6.5374
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1944160 37.1988 47.0295
Pocillopora_meandrina_HIv1___xfSc0000272 52107 505528 9.7017 11.37
Pocillopora_meandrina_HIv1___xfSc0000275 51938 387759 7.4658 7.9747
Pocillopora_meandrina_HIv1___xfSc0000284 51483 554821 10.7768 12.7526
Pocillopora_meandrina_HIv1___xfSc0000288 51367 536074 10.4362 16.1492
Pocillopora_meandrina_HIv1___xfSc0000300 50845 8439 0.166 0.525
Pocillopora_meandrina_HIv1___xfSc0000301 50809 360121 7.0877 8.4128
Pocillopora_meandrina_HIv1___xfSc0000343 49544 248733 5.0204 6.7646
Pocillopora_meandrina_HIv1___xfSc0000376 48519 351344 7.2414 15.5329
Pocillopora_meandrina_HIv1___xfSc0000415 47398 899722 18.9823 21.8956
Pocillopora_meandrina_HIv1___xfSc0000423 47202 72193 1.5294 3.2696
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1107410 23.5139 19.2792
Pocillopora_meandrina_HIv1___xfSc0000428 47057 784048 16.6617 21.7622
Pocillopora_meandrina_HIv1___xfSc0000436 46816 538184 11.4957 19.3174
Pocillopora_meandrina_HIv1___xfSc0000445 46561 295910 6.3553 6.8533
Pocillopora_meandrina_HIv1___xfSc0000447 46542 743338 15.9713 14.3169
Pocillopora_meandrina_HIv1___xfSc0000469 45938 598859 13.0362 10.7989
Pocillopora_meandrina_HIv1___xfSc0000477 45781 179213 3.9146 6.4612
Pocillopora_meandrina_HIv1___xfSc0000479 45736 186132 4.0697 6.0566
Pocillopora_meandrina_HIv1___xfSc0000482 45585 1071523 23.506 32.5662
Pocillopora_meandrina_HIv1___xfSc0000488 45379 79318 1.7479 3.6218
Pocillopora_meandrina_HIv1___xfSc0000506 44781 518629 11.5815 15.6473
Pocillopora_meandrina_HIv1___xfSc0000527 44235 331054 7.484 8.8529
Pocillopora_meandrina_HIv1___xfSc0000540 43935 369268 8.4049 9.9781
Pocillopora_meandrina_HIv1___xfSc0000555 43535 166660 3.8282 6.4058
Pocillopora_meandrina_HIv1___xfSc0000565 43357 524829 12.1048 10.4566
Pocillopora_meandrina_HIv1___xfSc0000566 43316 309208 7.1384 7.8089
Pocillopora_meandrina_HIv1___xfSc0000567 43305 197017 4.5495 8.5417
Pocillopora_meandrina_HIv1___xfSc0000570 43295 174110 4.0215 6.2209
Pocillopora_meandrina_HIv1___xfSc0000579 43029 78634 1.8275 4.1975
Pocillopora_meandrina_HIv1___xfSc0000583 42958 315061 7.3342 7.8172
Pocillopora_meandrina_HIv1___xfSc0000596 42675 302532 7.0892 10.0452
Pocillopora_meandrina_HIv1___xfSc0000612 42423 377987 8.91 6.8344
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2959330 69.8697 179.9631
Pocillopora_meandrina_HIv1___xfSc0000621 42164 283518 6.7242 8.2923
Pocillopora_meandrina_HIv1___xfSc0000642 41754 177553 4.2524 7.6498
Pocillopora_meandrina_HIv1___xfSc0000655 41446 133145 3.2125 5.7521
Pocillopora_meandrina_HIv1___xfSc0000692 40426 207888 5.1424 5.9978
Pocillopora_meandrina_HIv1___xfSc0000699 40296 42884 1.0642 2.457
Pocillopora_meandrina_HIv1___xfSc0000704 40233 500036 12.4285 15.2703
Pocillopora_meandrina_HIv1___xfSc0000705 40197 188803 4.6969 6.0011
Pocillopora_meandrina_HIv1___xfSc0000716 39998 365820 9.146 9.6899
Pocillopora_meandrina_HIv1___xfSc0000725 39827 322768 8.1043 16.7451
Pocillopora_meandrina_HIv1___xfSc0000729 39775 14775 0.3715 2.0706
Pocillopora_meandrina_HIv1___xfSc0000760 39228 20141 0.5134 1.3691
Pocillopora_meandrina_HIv1___xfSc0000763 39151 343787 8.7811 5.2508
Pocillopora_meandrina_HIv1___xfSc0000765 39117 223345 5.7097 8.5394
Pocillopora_meandrina_HIv1___xfSc0000788 38513 340200 8.8334 8.1208
Pocillopora_meandrina_HIv1___xfSc0000811 37888 265580 7.0096 6.7221
Pocillopora_meandrina_HIv1___xfSc0000812 37881 21059 0.5559 1.1299
Pocillopora_meandrina_HIv1___xfSc0000817 37779 547055 14.4804 8.595
Pocillopora_meandrina_HIv1___xfSc0000824 37656 107159 2.8457 4.5731
Pocillopora_meandrina_HIv1___xfSc0000835 37434 505762 13.5108 15.6505
Pocillopora_meandrina_HIv1___xfSc0000836 37372 217429 5.818 8.9582
Pocillopora_meandrina_HIv1___xfSc0000837 37368 455215 12.1819 10.7693
Pocillopora_meandrina_HIv1___xfSc0000840 37283 113769 3.0515 6.3767
Pocillopora_meandrina_HIv1___xfSc0000857 37006 104399 2.8211 4.5325
Pocillopora_meandrina_HIv1___xfSc0000859 36995 51658 1.3964 2.2149
Pocillopora_meandrina_HIv1___xfSc0000866 36925 133592 3.6179 4.9064
Pocillopora_meandrina_HIv1___xfSc0000868 36831 150036 4.0736 10.3573
Pocillopora_meandrina_HIv1___xfSc0000875 36611 62339 1.7027 4.4992
Pocillopora_meandrina_HIv1___xfSc0000885 36416 151482 4.1598 5.3977
Pocillopora_meandrina_HIv1___xfSc0000886 36355 100519 2.7649 5.1255
Pocillopora_meandrina_HIv1___xfSc0000890 36339 235616 6.4838 7.749
Pocillopora_meandrina_HIv1___xfSc0000892 36267 39718 1.0952 2.9307
Pocillopora_meandrina_HIv1___xfSc0000943 35168 18698 0.5317 1.7605
Pocillopora_meandrina_HIv1___xfSc0000948 35100 404722 11.5305 10.8929
Pocillopora_meandrina_HIv1___xfSc0000952 34934 506934 14.5112 9.9267
Pocillopora_meandrina_HIv1___xfSc0000953 34905 181419 5.1975 6.228
Pocillopora_meandrina_HIv1___xfSc0000957 34773 364882 10.4933 13.4872
Pocillopora_meandrina_HIv1___xfSc0000968 34345 63159 1.839 4.5903
Pocillopora_meandrina_HIv1___xfSc0000974 34140 325176 9.5248 8.4422
Pocillopora_meandrina_HIv1___xfSc0000975 33988 275861 8.1164 8.0786
Pocillopora_meandrina_HIv1___xfSc0000995 33324 129786 3.8947 9.3715
Pocillopora_meandrina_HIv1___xfSc0001011 32918 762714 23.1701 29.4895
Pocillopora_meandrina_HIv1___xfSc0001122 29140 341019 11.7028 8.361
Pocillopora_meandrina_HIv1___xfSc0001170 27381 84593 3.0895 4.6561
Pocillopora_meandrina_HIv1___xfSc0001179 27200 97977 3.6021 5.4119
Pocillopora_meandrina_HIv1___xfSc0001231 22938 38877 1.6949 3.3834
Pocillopora_meandrina_HIv1___xfSc0001237 22715 84666 3.7273 10.4081
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2317599 5.6766 9.6107
Pocillopora_meandrina_HIv1___xpSc0001275 48561 199111 4.1002 7.8591
Pocillopora_meandrina_HIv1___xpSc0001276 38618 77854 2.016 4.7634
Pocillopora_meandrina_HIv1___xpSc0001280 35955 288010 8.0103 10.8148
Pocillopora_meandrina_HIv1___xpSc0001281 34238 304597 8.8965 12.1572
Pocillopora_meandrina_HIv1___xpSc0001290 28931 428637 14.8158 10.5011
Pocillopora_meandrina_HIv1___xpSc0001321 15304 29938 1.9562 3.6721
Pocillopora_meandrina_HIv1___xpSc0001331 8958 157054 17.5323 10.362
Pocillopora_meandrina_HIv1___xpSc0001337 6786 76670 11.2983 5.966
Pocillopora_meandrina_HIv1___xpSc0001344 5647 72413 12.8233 14.8042
Pocillopora_meandrina_HIv1___xpSc0001355 3576 34842 9.7433 8.3351

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 21:38:18
    Generated by QualiMap v.2.3