Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-52-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-52-TP1_R1_001.fastp-trim.fq.gz -2 POC-52-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-52-TP1 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 19:58:41 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-52-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 35,156,612
Mapped reads 35,156,612 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 35,156,612 / 100%
Mapped reads, first in pair 17,578,306 / 50%
Mapped reads, second in pair 17,578,306 / 50%
Mapped reads, both in pair 35,156,612 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.57
Overlapping read pairs 12,308,460 / 70.02%
Duplicated reads (estimated) 3,149,090 / 8.96%
Duplication rate 8.69%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 1,870,805,884 / 40.33%
Number/percentage of C's 450,584,222 / 9.71%
Number/percentage of T's 1,871,628,166 / 40.35%
Number/percentage of G's 445,941,484 / 9.61%
Number/percentage of N's 87,538 / 0%
GC Percentage 19.33%

Coverage

Mean 12.3586
Standard Deviation 11.4423
Mean (paired-end reads overlap ignored) 9.94

Mapping Quality

Mean Mapping Quality 22.42

Insert size

Mean 234.16
Standard Deviation 83.53
P25/Median/P75 168 / 219 / 284

Mismatches and indels

General error rate 21.2%
Mismatches 964,641,940
Insertions 7,258,027
Mapped reads with at least one insertion 15.17%
Deletions 5,558,288
Mapped reads with at least one deletion 13.25%
Homopolymer indels 52.2%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 283279998 13.0838 9.7577
Pocillopora_meandrina_HIv1___Sc0000001 21507942 299863116 13.942 10.1218
Pocillopora_meandrina_HIv1___Sc0000002 19741974 272272502 13.7916 9.6097
Pocillopora_meandrina_HIv1___Sc0000003 19417450 237220863 12.2169 11.1678
Pocillopora_meandrina_HIv1___Sc0000004 14584444 175446136 12.0297 17.8237
Pocillopora_meandrina_HIv1___Sc0000005 14098929 186643567 13.2381 9.0848
Pocillopora_meandrina_HIv1___Sc0000006 14068054 185097777 13.1573 11.0614
Pocillopora_meandrina_HIv1___Sc0000007 13590779 175364088 12.9032 10.3876
Pocillopora_meandrina_HIv1___Sc0000008 12446599 176119680 14.15 10.2413
Pocillopora_meandrina_HIv1___Sc0000009 11983232 111482264 9.3032 15.5758
Pocillopora_meandrina_HIv1___Sc0000010 11763137 145353621 12.3567 11.9437
Pocillopora_meandrina_HIv1___Sc0000011 10501528 159998695 15.2358 9.4618
Pocillopora_meandrina_HIv1___Sc0000012 10024633 128968273 12.8651 11.2269
Pocillopora_meandrina_HIv1___Sc0000013 9946974 97429001 9.7948 9.9736
Pocillopora_meandrina_HIv1___Sc0000014 9536826 135503048 14.2084 9.6219
Pocillopora_meandrina_HIv1___Sc0000015 9393205 118010984 12.5634 9.5293
Pocillopora_meandrina_HIv1___Sc0000016 9288165 113458760 12.2154 9.5631
Pocillopora_meandrina_HIv1___Sc0000017 9274345 116015290 12.5093 9.7809
Pocillopora_meandrina_HIv1___Sc0000018 8584156 114468124 13.3348 9.3195
Pocillopora_meandrina_HIv1___Sc0000019 7112774 91761221 12.9009 10.5452
Pocillopora_meandrina_HIv1___Sc0000020 6748058 90740572 13.4469 12.4369
Pocillopora_meandrina_HIv1___Sc0000021 6546105 89950380 13.7411 9.4601
Pocillopora_meandrina_HIv1___Sc0000022 6319256 73594080 11.646 11.9139
Pocillopora_meandrina_HIv1___Sc0000023 5767069 62101428 10.7683 9.9749
Pocillopora_meandrina_HIv1___Sc0000024 5762297 48831020 8.4742 10.4068
Pocillopora_meandrina_HIv1___Sc0000025 5759531 66272541 11.5066 11.4455
Pocillopora_meandrina_HIv1___Sc0000026 5647578 84425648 14.949 10.0205
Pocillopora_meandrina_HIv1___Sc0000027 5550630 65290046 11.7626 14.86
Pocillopora_meandrina_HIv1___Sc0000028 5130920 71420681 13.9197 10.9189
Pocillopora_meandrina_HIv1___Sc0000029 4860867 51333859 10.5606 10.8245
Pocillopora_meandrina_HIv1___Sc0000030 4843735 67388679 13.9125 10.493
Pocillopora_meandrina_HIv1___Sc0000031 4691590 60778898 12.9549 10.2304
Pocillopora_meandrina_HIv1___Sc0000032 3615800 51362943 14.2051 11.7735
Pocillopora_meandrina_HIv1___Sc0000033 3306609 33959665 10.2702 11.3684
Pocillopora_meandrina_HIv1___Sc0000034 3122802 42443736 13.5916 9.7124
Pocillopora_meandrina_HIv1___Sc0000035 3015365 29883649 9.9105 14.6444
Pocillopora_meandrina_HIv1___Sc0000036 3007169 48723223 16.2024 9.894
Pocillopora_meandrina_HIv1___Sc0000037 2860435 35657521 12.4658 10.959
Pocillopora_meandrina_HIv1___Sc0000038 2701138 31278017 11.5796 11.4996
Pocillopora_meandrina_HIv1___Sc0000039 2599273 26513214 10.2002 13.6145
Pocillopora_meandrina_HIv1___Sc0000040 2445666 27324957 11.1728 10.8312
Pocillopora_meandrina_HIv1___Sc0000041 2159376 29941762 13.8659 11.1147
Pocillopora_meandrina_HIv1___Sc0000042 1957488 23464780 11.9872 9.8896
Pocillopora_meandrina_HIv1___Sc0000043 1845599 19843962 10.752 9.1201
Pocillopora_meandrina_HIv1___Sc0000044 1724711 23552406 13.6559 9.9512
Pocillopora_meandrina_HIv1___Sc0000045 1153740 12088321 10.4775 9.7559
Pocillopora_meandrina_HIv1___Sc0000046 755410 6737382 8.9188 11.5358
Pocillopora_meandrina_HIv1___Sc0000047 239089 111743 0.4674 1.7087
Pocillopora_meandrina_HIv1___Sc0000048 214660 33756 0.1573 1.0689
Pocillopora_meandrina_HIv1___Sc0000049 179266 600351 3.3489 7.3975
Pocillopora_meandrina_HIv1___Sc0000050 177168 143983 0.8127 2.0766
Pocillopora_meandrina_HIv1___Sc0000051 165057 674406 4.0859 7.1297
Pocillopora_meandrina_HIv1___Sc0000052 155210 15685 0.1011 1.0574
Pocillopora_meandrina_HIv1___Sc0000053 123249 181723 1.4744 4.6849
Pocillopora_meandrina_HIv1___Sc0000054 122643 1510475 12.316 23.8582
Pocillopora_meandrina_HIv1___Sc0000055 121609 416208 3.4225 7.6399
Pocillopora_meandrina_HIv1___Sc0000056 112816 44371 0.3933 3.8143
Pocillopora_meandrina_HIv1___Sc0000057 107171 353400 3.2975 7.4549
Pocillopora_meandrina_HIv1___Sc0000058 98341 26002 0.2644 2.8494
Pocillopora_meandrina_HIv1___Sc0000059 83292 1834 0.022 0.2069
Pocillopora_meandrina_HIv1___Sc0000060 79483 262 0.0033 0.0807
Pocillopora_meandrina_HIv1___Sc0000061 75390 319160 4.2335 9.9505
Pocillopora_meandrina_HIv1___Sc0000062 74194 11505 0.1551 0.7157
Pocillopora_meandrina_HIv1___Sc0000063 73457 40329 0.549 5.1722
Pocillopora_meandrina_HIv1___Sc0000064 72700 5031 0.0692 0.4225
Pocillopora_meandrina_HIv1___Sc0000065 67986 4776 0.0702 0.4907
Pocillopora_meandrina_HIv1___Sc0000066 66659 388453 5.8275 6.3488
Pocillopora_meandrina_HIv1___Sc0000067 64947 111431 1.7157 3.4658
Pocillopora_meandrina_HIv1___Sc0000068 64340 10132 0.1575 0.836
Pocillopora_meandrina_HIv1___Sc0000069 62616 137952 2.2031 6.0315
Pocillopora_meandrina_HIv1___Sc0000070 60121 32751 0.5448 2.5969
Pocillopora_meandrina_HIv1___Sc0000071 57157 31072 0.5436 1.3316
Pocillopora_meandrina_HIv1___Sc0000072 56626 11369 0.2008 2.3098
Pocillopora_meandrina_HIv1___Sc0000073 56082 12564 0.224 0.917
Pocillopora_meandrina_HIv1___Sc0000074 55210 249 0.0045 0.0921
Pocillopora_meandrina_HIv1___Sc0000075 54685 1085 0.0198 0.1475
Pocillopora_meandrina_HIv1___Sc0000076 54587 135894 2.4895 12.8367
Pocillopora_meandrina_HIv1___Sc0000077 53379 8226 0.1541 0.4516
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1874 0.0377 0.2747
Pocillopora_meandrina_HIv1___Sc0000080 47218 70750 1.4984 4.4453
Pocillopora_meandrina_HIv1___Sc0000081 42490 9222 0.217 0.6803
Pocillopora_meandrina_HIv1___Sc0000082 32657 486934 14.9106 34.8005
Pocillopora_meandrina_HIv1___Sc0000083 27992 2369 0.0846 0.4557
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 9693921 6.0526 10.4943
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3349878 2.7969 5.8539
Pocillopora_meandrina_HIv1___xfSc0000002 779520 4842275 6.2119 8.2273
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1290175 2.7905 5.9463
Pocillopora_meandrina_HIv1___xfSc0000004 334777 620934 1.8548 3.8832
Pocillopora_meandrina_HIv1___xfSc0000006 290100 481075 1.6583 3.3752
Pocillopora_meandrina_HIv1___xfSc0000007 252258 555879 2.2036 3.9823
Pocillopora_meandrina_HIv1___xfSc0000012 148278 381613 2.5736 5.3884
Pocillopora_meandrina_HIv1___xfSc0000014 118081 20884 0.1769 0.6898
Pocillopora_meandrina_HIv1___xfSc0000017 98555 536539 5.4441 84.9387
Pocillopora_meandrina_HIv1___xfSc0000021 95778 492745 5.1447 8.9858
Pocillopora_meandrina_HIv1___xfSc0000024 90744 461410 5.0847 7.7291
Pocillopora_meandrina_HIv1___xfSc0000029 85532 95945 1.1217 4.5097
Pocillopora_meandrina_HIv1___xfSc0000038 77395 73195 0.9457 11.3213
Pocillopora_meandrina_HIv1___xfSc0000058 69718 482216 6.9167 10.911
Pocillopora_meandrina_HIv1___xfSc0000059 69426 230999 3.3273 6.7846
Pocillopora_meandrina_HIv1___xfSc0000074 66573 421660 6.3338 7.6333
Pocillopora_meandrina_HIv1___xfSc0000081 65415 397124 6.0708 7.5714
Pocillopora_meandrina_HIv1___xfSc0000083 65317 679910 10.4094 12.0066
Pocillopora_meandrina_HIv1___xfSc0000092 63607 408913 6.4287 7.3472
Pocillopora_meandrina_HIv1___xfSc0000094 62842 52461 0.8348 2.2797
Pocillopora_meandrina_HIv1___xfSc0000113 60556 649121 10.7194 12.455
Pocillopora_meandrina_HIv1___xfSc0000132 59032 34877 0.5908 1.8261
Pocillopora_meandrina_HIv1___xfSc0000145 58221 216378 3.7165 4.7271
Pocillopora_meandrina_HIv1___xfSc0000146 58151 102432 1.7615 4.1565
Pocillopora_meandrina_HIv1___xfSc0000168 56681 271278 4.786 7.5187
Pocillopora_meandrina_HIv1___xfSc0000175 56271 197818 3.5155 9.9888
Pocillopora_meandrina_HIv1___xfSc0000195 55223 16096 0.2915 2.3123
Pocillopora_meandrina_HIv1___xfSc0000199 55095 356449 6.4697 13.565
Pocillopora_meandrina_HIv1___xfSc0000205 54658 41580 0.7607 1.8518
Pocillopora_meandrina_HIv1___xfSc0000206 54623 163096 2.9858 4.8261
Pocillopora_meandrina_HIv1___xfSc0000212 54299 265782 4.8948 6.9298
Pocillopora_meandrina_HIv1___xfSc0000217 54168 260945 4.8173 8.6636
Pocillopora_meandrina_HIv1___xfSc0000223 53823 423023 7.8595 7.4423
Pocillopora_meandrina_HIv1___xfSc0000228 53382 400020 7.4935 24.0977
Pocillopora_meandrina_HIv1___xfSc0000237 53049 200145 3.7728 5.9874
Pocillopora_meandrina_HIv1___xfSc0000262 52308 200312 3.8295 5.4228
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1411076 26.999 22.8148
Pocillopora_meandrina_HIv1___xfSc0000272 52107 205949 3.9524 6.5248
Pocillopora_meandrina_HIv1___xfSc0000275 51938 355186 6.8387 8.4859
Pocillopora_meandrina_HIv1___xfSc0000284 51483 384509 7.4687 9.5225
Pocillopora_meandrina_HIv1___xfSc0000288 51367 229012 4.4583 9.8608
Pocillopora_meandrina_HIv1___xfSc0000300 50845 13400 0.2635 1.0362
Pocillopora_meandrina_HIv1___xfSc0000301 50809 420253 8.2712 7.9732
Pocillopora_meandrina_HIv1___xfSc0000343 49544 123972 2.5023 4.9673
Pocillopora_meandrina_HIv1___xfSc0000376 48519 359606 7.4117 23.6863
Pocillopora_meandrina_HIv1___xfSc0000415 47398 211568 4.4636 5.4127
Pocillopora_meandrina_HIv1___xfSc0000423 47202 50548 1.0709 3.3674
Pocillopora_meandrina_HIv1___xfSc0000426 47096 834713 17.7236 19.3359
Pocillopora_meandrina_HIv1___xfSc0000428 47057 459542 9.7656 13.9996
Pocillopora_meandrina_HIv1___xfSc0000436 46816 219131 4.6807 11.4816
Pocillopora_meandrina_HIv1___xfSc0000445 46561 40384 0.8673 2.288
Pocillopora_meandrina_HIv1___xfSc0000447 46542 308691 6.6325 9.6453
Pocillopora_meandrina_HIv1___xfSc0000469 45938 267626 5.8258 5.8977
Pocillopora_meandrina_HIv1___xfSc0000477 45781 227539 4.9702 5.6643
Pocillopora_meandrina_HIv1___xfSc0000479 45736 127521 2.7882 4.6574
Pocillopora_meandrina_HIv1___xfSc0000482 45585 403829 8.8588 16.2938
Pocillopora_meandrina_HIv1___xfSc0000488 45379 175204 3.8609 5.6866
Pocillopora_meandrina_HIv1___xfSc0000506 44781 115583 2.5811 4.5412
Pocillopora_meandrina_HIv1___xfSc0000527 44235 169083 3.8224 6.1739
Pocillopora_meandrina_HIv1___xfSc0000540 43935 270339 6.1532 8.9479
Pocillopora_meandrina_HIv1___xfSc0000555 43535 180104 4.137 9.8916
Pocillopora_meandrina_HIv1___xfSc0000565 43357 289629 6.6801 6.8093
Pocillopora_meandrina_HIv1___xfSc0000566 43316 179735 4.1494 6.9908
Pocillopora_meandrina_HIv1___xfSc0000567 43305 149426 3.4505 6.751
Pocillopora_meandrina_HIv1___xfSc0000570 43295 71094 1.6421 4.4696
Pocillopora_meandrina_HIv1___xfSc0000579 43029 62505 1.4526 3.6416
Pocillopora_meandrina_HIv1___xfSc0000583 42958 255116 5.9387 6.4349
Pocillopora_meandrina_HIv1___xfSc0000596 42675 85335 1.9996 3.7237
Pocillopora_meandrina_HIv1___xfSc0000612 42423 116167 2.7383 4.3388
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2303659 54.3893 148.4887
Pocillopora_meandrina_HIv1___xfSc0000621 42164 233128 5.5291 6.8881
Pocillopora_meandrina_HIv1___xfSc0000642 41754 149428 3.5788 5.6555
Pocillopora_meandrina_HIv1___xfSc0000655 41446 425247 10.2603 19.9898
Pocillopora_meandrina_HIv1___xfSc0000692 40426 94922 2.348 3.937
Pocillopora_meandrina_HIv1___xfSc0000699 40296 34583 0.8582 2.1416
Pocillopora_meandrina_HIv1___xfSc0000704 40233 457223 11.3644 16.3602
Pocillopora_meandrina_HIv1___xfSc0000705 40197 85332 2.1228 4.6325
Pocillopora_meandrina_HIv1___xfSc0000716 39998 275872 6.8971 7.66
Pocillopora_meandrina_HIv1___xfSc0000725 39827 49151 1.2341 4.3929
Pocillopora_meandrina_HIv1___xfSc0000729 39775 66850 1.6807 14.7946
Pocillopora_meandrina_HIv1___xfSc0000760 39228 17785 0.4534 2.4464
Pocillopora_meandrina_HIv1___xfSc0000763 39151 185633 4.7415 5.4802
Pocillopora_meandrina_HIv1___xfSc0000765 39117 60236 1.5399 3.6335
Pocillopora_meandrina_HIv1___xfSc0000788 38513 188310 4.8895 6.9946
Pocillopora_meandrina_HIv1___xfSc0000811 37888 189363 4.998 4.8272
Pocillopora_meandrina_HIv1___xfSc0000812 37881 9866 0.2604 0.9954
Pocillopora_meandrina_HIv1___xfSc0000817 37779 326423 8.6403 7.4283
Pocillopora_meandrina_HIv1___xfSc0000824 37656 159060 4.224 5.764
Pocillopora_meandrina_HIv1___xfSc0000835 37434 235367 6.2875 7.6153
Pocillopora_meandrina_HIv1___xfSc0000836 37372 154791 4.1419 7.0961
Pocillopora_meandrina_HIv1___xfSc0000837 37368 130271 3.4862 6.501
Pocillopora_meandrina_HIv1___xfSc0000840 37283 311258 8.3485 14.8136
Pocillopora_meandrina_HIv1___xfSc0000857 37006 52529 1.4195 3.2333
Pocillopora_meandrina_HIv1___xfSc0000859 36995 35488 0.9593 1.7296
Pocillopora_meandrina_HIv1___xfSc0000866 36925 75968 2.0574 4.3536
Pocillopora_meandrina_HIv1___xfSc0000868 36831 99712 2.7073 5.793
Pocillopora_meandrina_HIv1___xfSc0000875 36611 9786 0.2673 0.8564
Pocillopora_meandrina_HIv1___xfSc0000885 36416 112539 3.0904 4.7436
Pocillopora_meandrina_HIv1___xfSc0000886 36355 206886 5.6907 9.4606
Pocillopora_meandrina_HIv1___xfSc0000890 36339 148499 4.0865 8.8972
Pocillopora_meandrina_HIv1___xfSc0000892 36267 16316 0.4499 1.4923
Pocillopora_meandrina_HIv1___xfSc0000943 35168 5112 0.1454 0.8081
Pocillopora_meandrina_HIv1___xfSc0000948 35100 169602 4.832 6.7135
Pocillopora_meandrina_HIv1___xfSc0000952 34934 69643 1.9936 4.2685
Pocillopora_meandrina_HIv1___xfSc0000953 34905 138480 3.9673 5.6724
Pocillopora_meandrina_HIv1___xfSc0000957 34773 206371 5.9348 10.1899
Pocillopora_meandrina_HIv1___xfSc0000968 34345 10583 0.3081 1.124
Pocillopora_meandrina_HIv1___xfSc0000974 34140 197817 5.7943 6.4956
Pocillopora_meandrina_HIv1___xfSc0000975 33988 307995 9.0619 9.8178
Pocillopora_meandrina_HIv1___xfSc0000995 33324 86391 2.5925 6.1441
Pocillopora_meandrina_HIv1___xfSc0001011 32918 114955 3.4922 7.3834
Pocillopora_meandrina_HIv1___xfSc0001122 29140 215364 7.3907 9.69
Pocillopora_meandrina_HIv1___xfSc0001170 27381 15885 0.5801 1.6893
Pocillopora_meandrina_HIv1___xfSc0001179 27200 69687 2.562 4.3578
Pocillopora_meandrina_HIv1___xfSc0001231 22938 12107 0.5278 1.1559
Pocillopora_meandrina_HIv1___xfSc0001237 22715 40325 1.7753 4.8201
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1688884 4.1367 7.7015
Pocillopora_meandrina_HIv1___xpSc0001275 48561 196167 4.0396 7.052
Pocillopora_meandrina_HIv1___xpSc0001276 38618 92884 2.4052 5.5379
Pocillopora_meandrina_HIv1___xpSc0001280 35955 131214 3.6494 5.6797
Pocillopora_meandrina_HIv1___xpSc0001281 34238 177004 5.1698 7.9963
Pocillopora_meandrina_HIv1___xpSc0001290 28931 196491 6.7917 8.1124
Pocillopora_meandrina_HIv1___xpSc0001321 15304 28579 1.8674 3.586
Pocillopora_meandrina_HIv1___xpSc0001331 8958 81126 9.0563 10.2204
Pocillopora_meandrina_HIv1___xpSc0001337 6786 8272 1.219 3.2266
Pocillopora_meandrina_HIv1___xpSc0001344 5647 35683 6.3189 8.3049
Pocillopora_meandrina_HIv1___xpSc0001355 3576 36406 10.1806 7.5524

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 19:58:43
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