Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-40-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-40-TP4_R1_001.fastp-trim.fq.gz -2 POC-40-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-40-TP4 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 23:12:46 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-40-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 41,161,754
Mapped reads 41,161,754 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 41,161,754 / 100%
Mapped reads, first in pair 20,580,877 / 50%
Mapped reads, second in pair 20,580,877 / 50%
Mapped reads, both in pair 41,161,754 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 133.21
Overlapping read pairs 10,620,795 / 51.61%
Duplicated reads (estimated) 3,869,690 / 9.4%
Duplication rate 9.2%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,204,498,524 / 40.4%
Number/percentage of C's 525,289,573 / 9.63%
Number/percentage of T's 2,206,755,650 / 40.44%
Number/percentage of G's 520,465,724 / 9.54%
Number/percentage of N's 103,042 / 0%
GC Percentage 19.16%

Coverage

Mean 14.5385
Standard Deviation 13.5214
Mean (paired-end reads overlap ignored) 12.77

Mapping Quality

Mean Mapping Quality 22.61

Insert size

Mean 272.39
Standard Deviation 90.56
P25/Median/P75 205 / 265 / 333

Mismatches and indels

General error rate 21.12%
Mismatches 1,130,178,116
Insertions 8,653,388
Mapped reads with at least one insertion 15.43%
Deletions 6,616,960
Mapped reads with at least one deletion 13.45%
Homopolymer indels 52.26%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 347557078 16.0526 11.8246
Pocillopora_meandrina_HIv1___Sc0000001 21507942 353046254 16.4147 11.4189
Pocillopora_meandrina_HIv1___Sc0000002 19741974 319167994 16.167 11.146
Pocillopora_meandrina_HIv1___Sc0000003 19417450 270442339 13.9278 12.4935
Pocillopora_meandrina_HIv1___Sc0000004 14584444 206728440 14.1746 18.6036
Pocillopora_meandrina_HIv1___Sc0000005 14098929 219178087 15.5457 10.456
Pocillopora_meandrina_HIv1___Sc0000006 14068054 218191235 15.5097 13.3043
Pocillopora_meandrina_HIv1___Sc0000007 13590779 207836208 15.2924 12.0046
Pocillopora_meandrina_HIv1___Sc0000008 12446599 205953391 16.547 11.3076
Pocillopora_meandrina_HIv1___Sc0000009 11983232 113809353 9.4974 14.5215
Pocillopora_meandrina_HIv1___Sc0000010 11763137 170009278 14.4527 13.9391
Pocillopora_meandrina_HIv1___Sc0000011 10501528 187201517 17.8261 9.895
Pocillopora_meandrina_HIv1___Sc0000012 10024633 149005780 14.864 14.8682
Pocillopora_meandrina_HIv1___Sc0000013 9946974 119306918 11.9943 11.5614
Pocillopora_meandrina_HIv1___Sc0000014 9536826 158552005 16.6252 10.6866
Pocillopora_meandrina_HIv1___Sc0000015 9393205 144516148 15.3852 11.8398
Pocillopora_meandrina_HIv1___Sc0000016 9288165 137708701 14.8263 11.4382
Pocillopora_meandrina_HIv1___Sc0000017 9274345 138882525 14.9749 11.1793
Pocillopora_meandrina_HIv1___Sc0000018 8584156 134855343 15.7098 11.023
Pocillopora_meandrina_HIv1___Sc0000019 7112774 103814699 14.5955 11.8457
Pocillopora_meandrina_HIv1___Sc0000020 6748058 101194209 14.996 11.7299
Pocillopora_meandrina_HIv1___Sc0000021 6546105 104526893 15.9678 10.9861
Pocillopora_meandrina_HIv1___Sc0000022 6319256 85648738 13.5536 13.8093
Pocillopora_meandrina_HIv1___Sc0000023 5767069 72588494 12.5867 11.3539
Pocillopora_meandrina_HIv1___Sc0000024 5762297 53053736 9.207 10.8871
Pocillopora_meandrina_HIv1___Sc0000025 5759531 79249094 13.7596 13.9078
Pocillopora_meandrina_HIv1___Sc0000026 5647578 100418491 17.7808 10.3276
Pocillopora_meandrina_HIv1___Sc0000027 5550630 88232953 15.896 19.914
Pocillopora_meandrina_HIv1___Sc0000028 5130920 82697121 16.1174 12.1153
Pocillopora_meandrina_HIv1___Sc0000029 4860867 59769438 12.296 10.9774
Pocillopora_meandrina_HIv1___Sc0000030 4843735 75921728 15.6742 10.4101
Pocillopora_meandrina_HIv1___Sc0000031 4691590 72911628 15.5409 10.6782
Pocillopora_meandrina_HIv1___Sc0000032 3615800 59174760 16.3656 11.4225
Pocillopora_meandrina_HIv1___Sc0000033 3306609 37939035 11.4737 11.5206
Pocillopora_meandrina_HIv1___Sc0000034 3122802 51463262 16.4798 11.1125
Pocillopora_meandrina_HIv1___Sc0000035 3015365 37656536 12.4882 13.1147
Pocillopora_meandrina_HIv1___Sc0000036 3007169 54288048 18.0529 10.1018
Pocillopora_meandrina_HIv1___Sc0000037 2860435 44421425 15.5296 14.295
Pocillopora_meandrina_HIv1___Sc0000038 2701138 37343752 13.8252 12.4792
Pocillopora_meandrina_HIv1___Sc0000039 2599273 32868646 12.6453 11.7299
Pocillopora_meandrina_HIv1___Sc0000040 2445666 36749840 15.0265 14.7128
Pocillopora_meandrina_HIv1___Sc0000041 2159376 34688590 16.0642 10.5036
Pocillopora_meandrina_HIv1___Sc0000042 1957488 24724874 12.6309 10.4906
Pocillopora_meandrina_HIv1___Sc0000043 1845599 23089381 12.5105 10.4759
Pocillopora_meandrina_HIv1___Sc0000044 1724711 27362778 15.8651 10.6708
Pocillopora_meandrina_HIv1___Sc0000045 1153740 13619323 11.8045 11.5261
Pocillopora_meandrina_HIv1___Sc0000046 755410 7995892 10.5848 16.1214
Pocillopora_meandrina_HIv1___Sc0000047 239089 141090 0.5901 1.8595
Pocillopora_meandrina_HIv1___Sc0000048 214660 53139 0.2475 1.3821
Pocillopora_meandrina_HIv1___Sc0000049 179266 501338 2.7966 6.8341
Pocillopora_meandrina_HIv1___Sc0000050 177168 329061 1.8573 4.5798
Pocillopora_meandrina_HIv1___Sc0000051 165057 620705 3.7605 6.7689
Pocillopora_meandrina_HIv1___Sc0000052 155210 32805 0.2114 2.4033
Pocillopora_meandrina_HIv1___Sc0000053 123249 171329 1.3901 3.5374
Pocillopora_meandrina_HIv1___Sc0000054 122643 1611809 13.1423 17.1469
Pocillopora_meandrina_HIv1___Sc0000055 121609 704180 5.7905 11.0915
Pocillopora_meandrina_HIv1___Sc0000056 112816 54821 0.4859 4.9827
Pocillopora_meandrina_HIv1___Sc0000057 107171 246057 2.2959 5.1449
Pocillopora_meandrina_HIv1___Sc0000058 98341 29061 0.2955 2.7181
Pocillopora_meandrina_HIv1___Sc0000059 83292 4856 0.0583 0.3611
Pocillopora_meandrina_HIv1___Sc0000060 79483 781 0.0098 0.1292
Pocillopora_meandrina_HIv1___Sc0000061 75390 397483 5.2724 12.489
Pocillopora_meandrina_HIv1___Sc0000062 74194 12097 0.163 0.7495
Pocillopora_meandrina_HIv1___Sc0000063 73457 120019 1.6339 13.2887
Pocillopora_meandrina_HIv1___Sc0000064 72700 17094 0.2351 1.1344
Pocillopora_meandrina_HIv1___Sc0000065 67986 13303 0.1957 1.5182
Pocillopora_meandrina_HIv1___Sc0000066 66659 451130 6.7677 7.0415
Pocillopora_meandrina_HIv1___Sc0000067 64947 104309 1.6061 3.7165
Pocillopora_meandrina_HIv1___Sc0000068 64340 5927 0.0921 0.5581
Pocillopora_meandrina_HIv1___Sc0000069 62616 176650 2.8212 7.2542
Pocillopora_meandrina_HIv1___Sc0000070 60121 276327 4.5962 28.3037
Pocillopora_meandrina_HIv1___Sc0000071 57157 91770 1.6056 2.9063
Pocillopora_meandrina_HIv1___Sc0000072 56626 12078 0.2133 2.2788
Pocillopora_meandrina_HIv1___Sc0000073 56082 18359 0.3274 1.1105
Pocillopora_meandrina_HIv1___Sc0000074 55210 0 0 0
Pocillopora_meandrina_HIv1___Sc0000075 54685 268 0.0049 0.0698
Pocillopora_meandrina_HIv1___Sc0000076 54587 175845 3.2214 15.2465
Pocillopora_meandrina_HIv1___Sc0000077 53379 15992 0.2996 0.827
Pocillopora_meandrina_HIv1___Sc0000078 51564 246 0.0048 0.0689
Pocillopora_meandrina_HIv1___Sc0000079 49664 543 0.0109 0.144
Pocillopora_meandrina_HIv1___Sc0000080 47218 66489 1.4081 3.4099
Pocillopora_meandrina_HIv1___Sc0000081 42490 13299 0.313 1.0522
Pocillopora_meandrina_HIv1___Sc0000082 32657 495456 15.1715 32.2591
Pocillopora_meandrina_HIv1___Sc0000083 27992 5309 0.1897 0.6781
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 7319421 4.57 7.7377
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3995165 3.3356 5.9766
Pocillopora_meandrina_HIv1___xfSc0000002 779520 9769633 12.5329 18.0309
Pocillopora_meandrina_HIv1___xfSc0000003 462347 2147063 4.6438 8.4204
Pocillopora_meandrina_HIv1___xfSc0000004 334777 642533 1.9193 3.7511
Pocillopora_meandrina_HIv1___xfSc0000006 290100 612520 2.1114 4.0055
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1009119 4.0003 6.9669
Pocillopora_meandrina_HIv1___xfSc0000012 148278 785578 5.298 8.3766
Pocillopora_meandrina_HIv1___xfSc0000014 118081 22709 0.1923 0.8261
Pocillopora_meandrina_HIv1___xfSc0000017 98555 424529 4.3075 61.8708
Pocillopora_meandrina_HIv1___xfSc0000021 95778 516186 5.3894 9.6177
Pocillopora_meandrina_HIv1___xfSc0000024 90744 294362 3.2439 6.4138
Pocillopora_meandrina_HIv1___xfSc0000029 85532 132004 1.5433 6.0119
Pocillopora_meandrina_HIv1___xfSc0000038 77395 43238 0.5587 3.9164
Pocillopora_meandrina_HIv1___xfSc0000058 69718 553268 7.9358 10.6019
Pocillopora_meandrina_HIv1___xfSc0000059 69426 280790 4.0445 7.2192
Pocillopora_meandrina_HIv1___xfSc0000074 66573 176715 2.6545 4.8607
Pocillopora_meandrina_HIv1___xfSc0000081 65415 480687 7.3483 9.0828
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1204715 18.4441 16.4986
Pocillopora_meandrina_HIv1___xfSc0000092 63607 462997 7.279 6.5361
Pocillopora_meandrina_HIv1___xfSc0000094 62842 170034 2.7057 5.4444
Pocillopora_meandrina_HIv1___xfSc0000113 60556 895873 14.7941 16.6693
Pocillopora_meandrina_HIv1___xfSc0000132 59032 29928 0.507 1.2713
Pocillopora_meandrina_HIv1___xfSc0000145 58221 277095 4.7594 5.8128
Pocillopora_meandrina_HIv1___xfSc0000146 58151 108817 1.8713 4.3739
Pocillopora_meandrina_HIv1___xfSc0000168 56681 319832 5.6427 8.8702
Pocillopora_meandrina_HIv1___xfSc0000175 56271 214427 3.8106 9.3901
Pocillopora_meandrina_HIv1___xfSc0000195 55223 15934 0.2885 2.2965
Pocillopora_meandrina_HIv1___xfSc0000199 55095 606452 11.0074 20.0918
Pocillopora_meandrina_HIv1___xfSc0000205 54658 121552 2.2239 4.2805
Pocillopora_meandrina_HIv1___xfSc0000206 54623 231877 4.245 6.481
Pocillopora_meandrina_HIv1___xfSc0000212 54299 291156 5.3621 8.7612
Pocillopora_meandrina_HIv1___xfSc0000217 54168 406958 7.5129 14.738
Pocillopora_meandrina_HIv1___xfSc0000223 53823 297555 5.5284 6.9114
Pocillopora_meandrina_HIv1___xfSc0000228 53382 405139 7.5894 23.2226
Pocillopora_meandrina_HIv1___xfSc0000237 53049 254610 4.7995 6.7042
Pocillopora_meandrina_HIv1___xfSc0000262 52308 432707 8.2723 8.3557
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1455796 27.8547 25.1578
Pocillopora_meandrina_HIv1___xfSc0000272 52107 296564 5.6914 8.8788
Pocillopora_meandrina_HIv1___xfSc0000275 51938 639222 12.3074 15.7081
Pocillopora_meandrina_HIv1___xfSc0000284 51483 604906 11.7496 14.0005
Pocillopora_meandrina_HIv1___xfSc0000288 51367 193494 3.7669 10.9161
Pocillopora_meandrina_HIv1___xfSc0000300 50845 10609 0.2087 0.7974
Pocillopora_meandrina_HIv1___xfSc0000301 50809 559811 11.0179 8.7365
Pocillopora_meandrina_HIv1___xfSc0000343 49544 201500 4.0671 7.9857
Pocillopora_meandrina_HIv1___xfSc0000376 48519 360210 7.4241 22.5696
Pocillopora_meandrina_HIv1___xfSc0000415 47398 337498 7.1205 8.0856
Pocillopora_meandrina_HIv1___xfSc0000423 47202 37676 0.7982 2.1909
Pocillopora_meandrina_HIv1___xfSc0000426 47096 994302 21.1122 25.9057
Pocillopora_meandrina_HIv1___xfSc0000428 47057 284155 6.0385 11.3007
Pocillopora_meandrina_HIv1___xfSc0000436 46816 290315 6.2012 10.8768
Pocillopora_meandrina_HIv1___xfSc0000445 46561 47867 1.028 2.9811
Pocillopora_meandrina_HIv1___xfSc0000447 46542 415363 8.9245 11.0359
Pocillopora_meandrina_HIv1___xfSc0000469 45938 304011 6.6179 6.9048
Pocillopora_meandrina_HIv1___xfSc0000477 45781 288653 6.3051 6.7206
Pocillopora_meandrina_HIv1___xfSc0000479 45736 188523 4.122 6.6285
Pocillopora_meandrina_HIv1___xfSc0000482 45585 272754 5.9834 10.2702
Pocillopora_meandrina_HIv1___xfSc0000488 45379 154854 3.4125 5.4162
Pocillopora_meandrina_HIv1___xfSc0000506 44781 186123 4.1563 6.1744
Pocillopora_meandrina_HIv1___xfSc0000527 44235 206728 4.6734 6.6932
Pocillopora_meandrina_HIv1___xfSc0000540 43935 351201 7.9936 10.1092
Pocillopora_meandrina_HIv1___xfSc0000555 43535 239353 5.4979 10.5903
Pocillopora_meandrina_HIv1___xfSc0000565 43357 272973 6.2959 6.0603
Pocillopora_meandrina_HIv1___xfSc0000566 43316 176117 4.0659 6.3101
Pocillopora_meandrina_HIv1___xfSc0000567 43305 146922 3.3927 6.4884
Pocillopora_meandrina_HIv1___xfSc0000570 43295 164608 3.802 9.6462
Pocillopora_meandrina_HIv1___xfSc0000579 43029 104946 2.439 5.6671
Pocillopora_meandrina_HIv1___xfSc0000583 42958 305505 7.1117 8.3612
Pocillopora_meandrina_HIv1___xfSc0000596 42675 199458 4.6739 7.4885
Pocillopora_meandrina_HIv1___xfSc0000612 42423 124477 2.9342 5.5771
Pocillopora_meandrina_HIv1___xfSc0000616 42355 5363090 126.6224 429.5568
Pocillopora_meandrina_HIv1___xfSc0000621 42164 284270 6.742 8.3991
Pocillopora_meandrina_HIv1___xfSc0000642 41754 146911 3.5185 6.6015
Pocillopora_meandrina_HIv1___xfSc0000655 41446 328061 7.9154 15.3139
Pocillopora_meandrina_HIv1___xfSc0000692 40426 252406 6.2437 7.9317
Pocillopora_meandrina_HIv1___xfSc0000699 40296 26734 0.6634 1.8835
Pocillopora_meandrina_HIv1___xfSc0000704 40233 387606 9.634 12.1944
Pocillopora_meandrina_HIv1___xfSc0000705 40197 131799 3.2788 5.9851
Pocillopora_meandrina_HIv1___xfSc0000716 39998 252036 6.3012 7.0247
Pocillopora_meandrina_HIv1___xfSc0000725 39827 77832 1.9543 6.3997
Pocillopora_meandrina_HIv1___xfSc0000729 39775 41712 1.0487 6.8403
Pocillopora_meandrina_HIv1___xfSc0000760 39228 11509 0.2934 1.2047
Pocillopora_meandrina_HIv1___xfSc0000763 39151 219273 5.6007 6.0373
Pocillopora_meandrina_HIv1___xfSc0000765 39117 90411 2.3113 5.8104
Pocillopora_meandrina_HIv1___xfSc0000788 38513 395000 10.2563 11.6898
Pocillopora_meandrina_HIv1___xfSc0000811 37888 328421 8.6682 8.4387
Pocillopora_meandrina_HIv1___xfSc0000812 37881 29415 0.7765 1.4
Pocillopora_meandrina_HIv1___xfSc0000817 37779 328188 8.687 7.1754
Pocillopora_meandrina_HIv1___xfSc0000824 37656 240927 6.3981 10.2397
Pocillopora_meandrina_HIv1___xfSc0000835 37434 116903 3.1229 4.964
Pocillopora_meandrina_HIv1___xfSc0000836 37372 237955 6.3672 9.2152
Pocillopora_meandrina_HIv1___xfSc0000837 37368 416497 11.1458 10.3449
Pocillopora_meandrina_HIv1___xfSc0000840 37283 242684 6.5092 14.976
Pocillopora_meandrina_HIv1___xfSc0000857 37006 134627 3.638 4.9035
Pocillopora_meandrina_HIv1___xfSc0000859 36995 34875 0.9427 1.8867
Pocillopora_meandrina_HIv1___xfSc0000866 36925 30440 0.8244 1.6841
Pocillopora_meandrina_HIv1___xfSc0000868 36831 113024 3.0687 6.1439
Pocillopora_meandrina_HIv1___xfSc0000875 36611 30508 0.8333 2.1165
Pocillopora_meandrina_HIv1___xfSc0000885 36416 177743 4.8809 6.8125
Pocillopora_meandrina_HIv1___xfSc0000886 36355 103742 2.8536 4.2858
Pocillopora_meandrina_HIv1___xfSc0000890 36339 183687 5.0548 10.4745
Pocillopora_meandrina_HIv1___xfSc0000892 36267 113230 3.1221 19.3951
Pocillopora_meandrina_HIv1___xfSc0000943 35168 10394 0.2956 1.3511
Pocillopora_meandrina_HIv1___xfSc0000948 35100 219246 6.2463 8.0705
Pocillopora_meandrina_HIv1___xfSc0000952 34934 400445 11.4629 8.5509
Pocillopora_meandrina_HIv1___xfSc0000953 34905 158430 4.5389 6.0339
Pocillopora_meandrina_HIv1___xfSc0000957 34773 155552 4.4734 7.9591
Pocillopora_meandrina_HIv1___xfSc0000968 34345 12541 0.3651 1.3162
Pocillopora_meandrina_HIv1___xfSc0000974 34140 243366 7.1285 8.8077
Pocillopora_meandrina_HIv1___xfSc0000975 33988 250820 7.3797 6.8841
Pocillopora_meandrina_HIv1___xfSc0000995 33324 80138 2.4048 5.9495
Pocillopora_meandrina_HIv1___xfSc0001011 32918 136119 4.1351 6.4965
Pocillopora_meandrina_HIv1___xfSc0001122 29140 268762 9.2231 8.8063
Pocillopora_meandrina_HIv1___xfSc0001170 27381 18050 0.6592 1.7677
Pocillopora_meandrina_HIv1___xfSc0001179 27200 80886 2.9737 5.1306
Pocillopora_meandrina_HIv1___xfSc0001231 22938 21699 0.946 1.6121
Pocillopora_meandrina_HIv1___xfSc0001237 22715 94745 4.171 11.4654
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2125242 5.2055 8.4048
Pocillopora_meandrina_HIv1___xpSc0001275 48561 194446 4.0042 7.9901
Pocillopora_meandrina_HIv1___xpSc0001276 38618 77342 2.0027 6.7622
Pocillopora_meandrina_HIv1___xpSc0001280 35955 112048 3.1163 4.6212
Pocillopora_meandrina_HIv1___xpSc0001281 34238 172005 5.0238 8.0213
Pocillopora_meandrina_HIv1___xpSc0001290 28931 118849 4.108 5.4253
Pocillopora_meandrina_HIv1___xpSc0001321 15304 46110 3.0129 6.655
Pocillopora_meandrina_HIv1___xpSc0001331 8958 132878 14.8334 9.2282
Pocillopora_meandrina_HIv1___xpSc0001337 6786 83381 12.2872 5.3807
Pocillopora_meandrina_HIv1___xpSc0001344 5647 55655 9.8557 12.9107
Pocillopora_meandrina_HIv1___xpSc0001355 3576 46093 12.8895 10.2024

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 23:12:47
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