Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-40-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-40-TP2_R1_001.fastp-trim.fq.gz -2 POC-40-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-40-TP2 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:43:57 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-40-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 52,664,676
Mapped reads 52,664,676 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 52,664,676 / 100%
Mapped reads, first in pair 26,332,338 / 50%
Mapped reads, second in pair 26,332,338 / 50%
Mapped reads, both in pair 52,664,676 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.1
Overlapping read pairs 13,501,277 / 51.27%
Duplicated reads (estimated) 6,237,999 / 11.84%
Duplication rate 11.6%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,819,205,748 / 40.4%
Number/percentage of C's 671,220,880 / 9.62%
Number/percentage of T's 2,822,278,649 / 40.44%
Number/percentage of G's 665,459,603 / 9.54%
Number/percentage of N's 132,829 / 0%
GC Percentage 19.15%

Coverage

Mean 18.5908
Standard Deviation 17.0078
Mean (paired-end reads overlap ignored) 16.25

Mapping Quality

Mean Mapping Quality 22.73

Insert size

Mean 272.29
Standard Deviation 92.4
P25/Median/P75 201 / 265 / 337

Mismatches and indels

General error rate 21.08%
Mismatches 1,444,387,875
Insertions 10,528,394
Mapped reads with at least one insertion 15.06%
Deletions 8,379,163
Mapped reads with at least one deletion 13.34%
Homopolymer indels 52.33%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 444192116 20.5159 14.855
Pocillopora_meandrina_HIv1___Sc0000001 21507942 451109125 20.9741 14.3991
Pocillopora_meandrina_HIv1___Sc0000002 19741974 410213367 20.7787 14.0755
Pocillopora_meandrina_HIv1___Sc0000003 19417450 345623083 17.7996 15.8736
Pocillopora_meandrina_HIv1___Sc0000004 14584444 262737014 18.0149 22.479
Pocillopora_meandrina_HIv1___Sc0000005 14098929 279467602 19.8219 13.162
Pocillopora_meandrina_HIv1___Sc0000006 14068054 279898783 19.8961 16.6258
Pocillopora_meandrina_HIv1___Sc0000007 13590779 266267521 19.5918 15.0357
Pocillopora_meandrina_HIv1___Sc0000008 12446599 263953161 21.2069 14.2049
Pocillopora_meandrina_HIv1___Sc0000009 11983232 144006508 12.0173 18.1502
Pocillopora_meandrina_HIv1___Sc0000010 11763137 217159288 18.461 17.2569
Pocillopora_meandrina_HIv1___Sc0000011 10501528 240211200 22.8739 12.4155
Pocillopora_meandrina_HIv1___Sc0000012 10024633 190029179 18.9562 18.6261
Pocillopora_meandrina_HIv1___Sc0000013 9946974 152852845 15.3668 14.5655
Pocillopora_meandrina_HIv1___Sc0000014 9536826 202190440 21.201 13.3693
Pocillopora_meandrina_HIv1___Sc0000015 9393205 184912247 19.6857 14.8913
Pocillopora_meandrina_HIv1___Sc0000016 9288165 176104309 18.9601 14.3609
Pocillopora_meandrina_HIv1___Sc0000017 9274345 178300419 19.2251 14.1835
Pocillopora_meandrina_HIv1___Sc0000018 8584156 172973834 20.1504 13.8082
Pocillopora_meandrina_HIv1___Sc0000019 7112774 132552540 18.6358 14.8349
Pocillopora_meandrina_HIv1___Sc0000020 6748058 129335666 19.1664 14.813
Pocillopora_meandrina_HIv1___Sc0000021 6546105 133536785 20.3994 13.7659
Pocillopora_meandrina_HIv1___Sc0000022 6319256 109826040 17.3796 17.359
Pocillopora_meandrina_HIv1___Sc0000023 5767069 92624741 16.061 14.2886
Pocillopora_meandrina_HIv1___Sc0000024 5762297 67168905 11.6566 13.7038
Pocillopora_meandrina_HIv1___Sc0000025 5759531 101240771 17.578 17.7491
Pocillopora_meandrina_HIv1___Sc0000026 5647578 129042236 22.8491 13.1613
Pocillopora_meandrina_HIv1___Sc0000027 5550630 112398002 20.2496 25.3088
Pocillopora_meandrina_HIv1___Sc0000028 5130920 106292700 20.7161 15.4286
Pocillopora_meandrina_HIv1___Sc0000029 4860867 76170381 15.6701 13.8971
Pocillopora_meandrina_HIv1___Sc0000030 4843735 96731354 19.9704 13.1434
Pocillopora_meandrina_HIv1___Sc0000031 4691590 93606090 19.9519 13.6142
Pocillopora_meandrina_HIv1___Sc0000032 3615800 75543813 20.8927 14.4158
Pocillopora_meandrina_HIv1___Sc0000033 3306609 48440303 14.6495 14.4207
Pocillopora_meandrina_HIv1___Sc0000034 3122802 66004423 21.1363 13.9949
Pocillopora_meandrina_HIv1___Sc0000035 3015365 47998149 15.9179 16.8472
Pocillopora_meandrina_HIv1___Sc0000036 3007169 69694439 23.1761 12.6562
Pocillopora_meandrina_HIv1___Sc0000037 2860435 57032251 19.9383 17.8476
Pocillopora_meandrina_HIv1___Sc0000038 2701138 47759220 17.6811 15.756
Pocillopora_meandrina_HIv1___Sc0000039 2599273 42021953 16.1668 15.1447
Pocillopora_meandrina_HIv1___Sc0000040 2445666 46676446 19.0854 18.4597
Pocillopora_meandrina_HIv1___Sc0000041 2159376 44466621 20.5923 13.4884
Pocillopora_meandrina_HIv1___Sc0000042 1957488 31941201 16.3174 13.2545
Pocillopora_meandrina_HIv1___Sc0000043 1845599 29632545 16.0558 13.2423
Pocillopora_meandrina_HIv1___Sc0000044 1724711 34899609 20.235 13.3549
Pocillopora_meandrina_HIv1___Sc0000045 1153740 17451431 15.126 14.3851
Pocillopora_meandrina_HIv1___Sc0000046 755410 10208074 13.5133 20.5015
Pocillopora_meandrina_HIv1___Sc0000047 239089 185809 0.7772 2.4353
Pocillopora_meandrina_HIv1___Sc0000048 214660 65746 0.3063 1.8736
Pocillopora_meandrina_HIv1___Sc0000049 179266 614691 3.4289 8.3438
Pocillopora_meandrina_HIv1___Sc0000050 177168 391532 2.2099 5.4756
Pocillopora_meandrina_HIv1___Sc0000051 165057 827220 5.0117 8.5764
Pocillopora_meandrina_HIv1___Sc0000052 155210 39502 0.2545 2.8989
Pocillopora_meandrina_HIv1___Sc0000053 123249 217223 1.7625 4.3836
Pocillopora_meandrina_HIv1___Sc0000054 122643 2066047 16.846 21.5537
Pocillopora_meandrina_HIv1___Sc0000055 121609 895665 7.3651 13.5326
Pocillopora_meandrina_HIv1___Sc0000056 112816 71785 0.6363 6.5859
Pocillopora_meandrina_HIv1___Sc0000057 107171 284493 2.6546 6.4757
Pocillopora_meandrina_HIv1___Sc0000058 98341 37295 0.3792 3.4851
Pocillopora_meandrina_HIv1___Sc0000059 83292 5862 0.0704 0.3419
Pocillopora_meandrina_HIv1___Sc0000060 79483 523 0.0066 0.0863
Pocillopora_meandrina_HIv1___Sc0000061 75390 501887 6.6572 16.2903
Pocillopora_meandrina_HIv1___Sc0000062 74194 13684 0.1844 0.7077
Pocillopora_meandrina_HIv1___Sc0000063 73457 141615 1.9279 15.6433
Pocillopora_meandrina_HIv1___Sc0000064 72700 24593 0.3383 1.2701
Pocillopora_meandrina_HIv1___Sc0000065 67986 13013 0.1914 1.6976
Pocillopora_meandrina_HIv1___Sc0000066 66659 562453 8.4378 8.8807
Pocillopora_meandrina_HIv1___Sc0000067 64947 130920 2.0158 4.742
Pocillopora_meandrina_HIv1___Sc0000068 64340 12817 0.1992 1.0749
Pocillopora_meandrina_HIv1___Sc0000069 62616 228553 3.6501 9.4807
Pocillopora_meandrina_HIv1___Sc0000070 60121 324225 5.3929 31.5574
Pocillopora_meandrina_HIv1___Sc0000071 57157 103348 1.8081 2.9297
Pocillopora_meandrina_HIv1___Sc0000072 56626 18384 0.3247 3.4021
Pocillopora_meandrina_HIv1___Sc0000073 56082 21087 0.376 1.1139
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 2140 0.0391 0.2684
Pocillopora_meandrina_HIv1___Sc0000076 54587 222707 4.0799 20.1015
Pocillopora_meandrina_HIv1___Sc0000077 53379 26159 0.4901 1.2902
Pocillopora_meandrina_HIv1___Sc0000078 51564 517 0.01 0.1256
Pocillopora_meandrina_HIv1___Sc0000079 49664 2680 0.054 0.4085
Pocillopora_meandrina_HIv1___Sc0000080 47218 81828 1.733 4.4938
Pocillopora_meandrina_HIv1___Sc0000081 42490 13761 0.3239 1.0748
Pocillopora_meandrina_HIv1___Sc0000082 32657 572170 17.5206 36.6777
Pocillopora_meandrina_HIv1___Sc0000083 27992 3738 0.1335 0.6324
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 9272738 5.7896 9.6592
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 5037632 4.206 7.4694
Pocillopora_meandrina_HIv1___xfSc0000002 779520 12401540 15.9092 22.7087
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2700120 5.84 10.5347
Pocillopora_meandrina_HIv1___xfSc0000004 334777 859118 2.5662 4.7702
Pocillopora_meandrina_HIv1___xfSc0000006 290100 775922 2.6747 5.1017
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1282828 5.0854 8.4991
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1037818 6.9991 11.1289
Pocillopora_meandrina_HIv1___xfSc0000014 118081 31922 0.2703 1.0737
Pocillopora_meandrina_HIv1___xfSc0000017 98555 568353 5.7669 82.6484
Pocillopora_meandrina_HIv1___xfSc0000021 95778 653881 6.827 11.64
Pocillopora_meandrina_HIv1___xfSc0000024 90744 386814 4.2627 8.3295
Pocillopora_meandrina_HIv1___xfSc0000029 85532 167283 1.9558 7.518
Pocillopora_meandrina_HIv1___xfSc0000038 77395 54494 0.7041 4.4436
Pocillopora_meandrina_HIv1___xfSc0000058 69718 677911 9.7236 13.0405
Pocillopora_meandrina_HIv1___xfSc0000059 69426 392343 5.6512 10.2765
Pocillopora_meandrina_HIv1___xfSc0000074 66573 231610 3.479 5.6004
Pocillopora_meandrina_HIv1___xfSc0000081 65415 613010 9.3711 11.5755
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1573773 24.0944 21.5365
Pocillopora_meandrina_HIv1___xfSc0000092 63607 569798 8.9581 7.8274
Pocillopora_meandrina_HIv1___xfSc0000094 62842 202564 3.2234 6.403
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1113183 18.3827 20.749
Pocillopora_meandrina_HIv1___xfSc0000132 59032 41576 0.7043 1.9402
Pocillopora_meandrina_HIv1___xfSc0000145 58221 370263 6.3596 7.4993
Pocillopora_meandrina_HIv1___xfSc0000146 58151 130451 2.2433 4.6222
Pocillopora_meandrina_HIv1___xfSc0000168 56681 396108 6.9884 10.8904
Pocillopora_meandrina_HIv1___xfSc0000175 56271 278657 4.9521 11.9806
Pocillopora_meandrina_HIv1___xfSc0000195 55223 18350 0.3323 2.5111
Pocillopora_meandrina_HIv1___xfSc0000199 55095 802820 14.5716 26.6675
Pocillopora_meandrina_HIv1___xfSc0000205 54658 141500 2.5888 4.7802
Pocillopora_meandrina_HIv1___xfSc0000206 54623 285290 5.2229 7.8169
Pocillopora_meandrina_HIv1___xfSc0000212 54299 385982 7.1085 11.7207
Pocillopora_meandrina_HIv1___xfSc0000217 54168 528852 9.7632 20.424
Pocillopora_meandrina_HIv1___xfSc0000223 53823 361812 6.7223 8.3988
Pocillopora_meandrina_HIv1___xfSc0000228 53382 484527 9.0766 27.8647
Pocillopora_meandrina_HIv1___xfSc0000237 53049 319434 6.0215 8.4032
Pocillopora_meandrina_HIv1___xfSc0000262 52308 545033 10.4197 10.9454
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1813448 34.6978 31.3752
Pocillopora_meandrina_HIv1___xfSc0000272 52107 371257 7.1249 11.0542
Pocillopora_meandrina_HIv1___xfSc0000275 51938 810671 15.6084 19.0572
Pocillopora_meandrina_HIv1___xfSc0000284 51483 816137 15.8526 18.3722
Pocillopora_meandrina_HIv1___xfSc0000288 51367 248177 4.8314 13.9211
Pocillopora_meandrina_HIv1___xfSc0000300 50845 16640 0.3273 1.1573
Pocillopora_meandrina_HIv1___xfSc0000301 50809 762867 15.0144 11.5752
Pocillopora_meandrina_HIv1___xfSc0000343 49544 254890 5.1447 9.4465
Pocillopora_meandrina_HIv1___xfSc0000376 48519 476314 9.8171 29.4279
Pocillopora_meandrina_HIv1___xfSc0000415 47398 394775 8.3289 9.5258
Pocillopora_meandrina_HIv1___xfSc0000423 47202 48899 1.036 2.9109
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1219502 25.894 31.7821
Pocillopora_meandrina_HIv1___xfSc0000428 47057 339827 7.2216 13.1461
Pocillopora_meandrina_HIv1___xfSc0000436 46816 367617 7.8524 13.8983
Pocillopora_meandrina_HIv1___xfSc0000445 46561 59056 1.2684 3.8314
Pocillopora_meandrina_HIv1___xfSc0000447 46542 511889 10.9984 13.7659
Pocillopora_meandrina_HIv1___xfSc0000469 45938 375161 8.1667 8.5463
Pocillopora_meandrina_HIv1___xfSc0000477 45781 370454 8.0919 8.3562
Pocillopora_meandrina_HIv1___xfSc0000479 45736 221230 4.8371 7.4277
Pocillopora_meandrina_HIv1___xfSc0000482 45585 342889 7.522 13.622
Pocillopora_meandrina_HIv1___xfSc0000488 45379 191901 4.2289 7.1749
Pocillopora_meandrina_HIv1___xfSc0000506 44781 249640 5.5747 8.1611
Pocillopora_meandrina_HIv1___xfSc0000527 44235 257777 5.8274 8.3448
Pocillopora_meandrina_HIv1___xfSc0000540 43935 442015 10.0607 12.9884
Pocillopora_meandrina_HIv1___xfSc0000555 43535 299985 6.8907 12.651
Pocillopora_meandrina_HIv1___xfSc0000565 43357 348509 8.0381 7.5882
Pocillopora_meandrina_HIv1___xfSc0000566 43316 261007 6.0256 9.2087
Pocillopora_meandrina_HIv1___xfSc0000567 43305 169965 3.9248 7.8393
Pocillopora_meandrina_HIv1___xfSc0000570 43295 204608 4.7259 11.6861
Pocillopora_meandrina_HIv1___xfSc0000579 43029 123992 2.8816 6.347
Pocillopora_meandrina_HIv1___xfSc0000583 42958 405452 9.4383 10.7394
Pocillopora_meandrina_HIv1___xfSc0000596 42675 282427 6.6181 10.1328
Pocillopora_meandrina_HIv1___xfSc0000612 42423 152057 3.5843 6.6837
Pocillopora_meandrina_HIv1___xfSc0000616 42355 7093370 167.4742 542.8274
Pocillopora_meandrina_HIv1___xfSc0000621 42164 364149 8.6365 10.2823
Pocillopora_meandrina_HIv1___xfSc0000642 41754 187063 4.4801 7.9347
Pocillopora_meandrina_HIv1___xfSc0000655 41446 437206 10.5488 19.4032
Pocillopora_meandrina_HIv1___xfSc0000692 40426 324846 8.0356 9.3659
Pocillopora_meandrina_HIv1___xfSc0000699 40296 42611 1.0574 2.235
Pocillopora_meandrina_HIv1___xfSc0000704 40233 487666 12.121 15.0248
Pocillopora_meandrina_HIv1___xfSc0000705 40197 155444 3.8671 7.1036
Pocillopora_meandrina_HIv1___xfSc0000716 39998 338752 8.4692 9.4068
Pocillopora_meandrina_HIv1___xfSc0000725 39827 101579 2.5505 7.5328
Pocillopora_meandrina_HIv1___xfSc0000729 39775 53885 1.3547 9.6836
Pocillopora_meandrina_HIv1___xfSc0000760 39228 15858 0.4043 1.5695
Pocillopora_meandrina_HIv1___xfSc0000763 39151 297966 7.6107 7.7523
Pocillopora_meandrina_HIv1___xfSc0000765 39117 114128 2.9176 7.1999
Pocillopora_meandrina_HIv1___xfSc0000788 38513 479947 12.4619 14.9959
Pocillopora_meandrina_HIv1___xfSc0000811 37888 398656 10.522 9.2377
Pocillopora_meandrina_HIv1___xfSc0000812 37881 42738 1.1282 2.1323
Pocillopora_meandrina_HIv1___xfSc0000817 37779 399286 10.569 8.5812
Pocillopora_meandrina_HIv1___xfSc0000824 37656 319234 8.4776 13.3159
Pocillopora_meandrina_HIv1___xfSc0000835 37434 144927 3.8715 6.2071
Pocillopora_meandrina_HIv1___xfSc0000836 37372 311121 8.325 12.0256
Pocillopora_meandrina_HIv1___xfSc0000837 37368 500806 13.402 12.2514
Pocillopora_meandrina_HIv1___xfSc0000840 37283 291670 7.8231 18.4241
Pocillopora_meandrina_HIv1___xfSc0000857 37006 179313 4.8455 6.1794
Pocillopora_meandrina_HIv1___xfSc0000859 36995 55105 1.4895 2.4241
Pocillopora_meandrina_HIv1___xfSc0000866 36925 33274 0.9011 1.9011
Pocillopora_meandrina_HIv1___xfSc0000868 36831 125921 3.4189 7.2342
Pocillopora_meandrina_HIv1___xfSc0000875 36611 28528 0.7792 2.2524
Pocillopora_meandrina_HIv1___xfSc0000885 36416 235152 6.4574 8.066
Pocillopora_meandrina_HIv1___xfSc0000886 36355 131961 3.6298 5.1545
Pocillopora_meandrina_HIv1___xfSc0000890 36339 228629 6.2916 14.3923
Pocillopora_meandrina_HIv1___xfSc0000892 36267 139243 3.8394 23.5861
Pocillopora_meandrina_HIv1___xfSc0000943 35168 9135 0.2598 1.2124
Pocillopora_meandrina_HIv1___xfSc0000948 35100 267751 7.6282 9.7416
Pocillopora_meandrina_HIv1___xfSc0000952 34934 489523 14.0128 10.2585
Pocillopora_meandrina_HIv1___xfSc0000953 34905 205274 5.8809 7.8244
Pocillopora_meandrina_HIv1___xfSc0000957 34773 187954 5.4052 9.7188
Pocillopora_meandrina_HIv1___xfSc0000968 34345 13042 0.3797 1.6493
Pocillopora_meandrina_HIv1___xfSc0000974 34140 345203 10.1114 11.8641
Pocillopora_meandrina_HIv1___xfSc0000975 33988 309920 9.1185 8.6543
Pocillopora_meandrina_HIv1___xfSc0000995 33324 111277 3.3392 8.0117
Pocillopora_meandrina_HIv1___xfSc0001011 32918 165196 5.0184 7.6704
Pocillopora_meandrina_HIv1___xfSc0001122 29140 331731 11.384 10.3093
Pocillopora_meandrina_HIv1___xfSc0001170 27381 23747 0.8673 2.286
Pocillopora_meandrina_HIv1___xfSc0001179 27200 109522 4.0265 7.0489
Pocillopora_meandrina_HIv1___xfSc0001231 22938 26072 1.1366 1.9356
Pocillopora_meandrina_HIv1___xfSc0001237 22715 114330 5.0332 13.8699
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2697415 6.6069 10.5215
Pocillopora_meandrina_HIv1___xpSc0001275 48561 216404 4.4563 8.5187
Pocillopora_meandrina_HIv1___xpSc0001276 38618 96520 2.4994 8.2775
Pocillopora_meandrina_HIv1___xpSc0001280 35955 151790 4.2217 5.9583
Pocillopora_meandrina_HIv1___xpSc0001281 34238 221936 6.4822 10.1953
Pocillopora_meandrina_HIv1___xpSc0001290 28931 174898 6.0453 7.7552
Pocillopora_meandrina_HIv1___xpSc0001321 15304 56571 3.6965 7.6773
Pocillopora_meandrina_HIv1___xpSc0001331 8958 161481 18.0265 10.9625
Pocillopora_meandrina_HIv1___xpSc0001337 6786 105803 15.5914 6.4333
Pocillopora_meandrina_HIv1___xpSc0001344 5647 66642 11.8013 13.2698
Pocillopora_meandrina_HIv1___xpSc0001355 3576 61430 17.1784 13.4578

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 21:43:59
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