Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-219-TP1.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-219-TP1_R1_001.fastp-trim.fq.gz -2 POC-219-TP1_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-219-TP1 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:32:24 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-219-TP1.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 38,125,776
Mapped reads 38,125,776 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 38,125,776 / 100%
Mapped reads, first in pair 19,062,888 / 50%
Mapped reads, second in pair 19,062,888 / 50%
Mapped reads, both in pair 38,125,776 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.54
Overlapping read pairs 12,451,229 / 65.32%
Duplicated reads (estimated) 3,990,929 / 10.47%
Duplication rate 10.06%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,003,488,152 / 40.13%
Number/percentage of C's 497,742,532 / 9.97%
Number/percentage of T's 2,004,634,049 / 40.15%
Number/percentage of G's 486,818,020 / 9.75%
Number/percentage of N's 394,152 / 0.01%
GC Percentage 19.72%

Coverage

Mean 13.3013
Standard Deviation 13.264
Mean (paired-end reads overlap ignored) 10.89

Mapping Quality

Mean Mapping Quality 22.5

Insert size

Mean 238.56
Standard Deviation 86.95
P25/Median/P75 165 / 231 / 296

Mismatches and indels

General error rate 21.56%
Mismatches 1,058,265,055
Insertions 7,369,614
Mapped reads with at least one insertion 14.51%
Deletions 5,926,664
Mapped reads with at least one deletion 12.99%
Homopolymer indels 51.57%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 308771415 14.2612 11.2753
Pocillopora_meandrina_HIv1___Sc0000001 21507942 325510629 15.1344 10.7989
Pocillopora_meandrina_HIv1___Sc0000002 19741974 286536687 14.5141 10.3709
Pocillopora_meandrina_HIv1___Sc0000003 19417450 254409576 13.1021 11.9545
Pocillopora_meandrina_HIv1___Sc0000004 14584444 195115925 13.3784 29.2593
Pocillopora_meandrina_HIv1___Sc0000005 14098929 198929818 14.1096 10.0535
Pocillopora_meandrina_HIv1___Sc0000006 14068054 200568837 14.257 11.9097
Pocillopora_meandrina_HIv1___Sc0000007 13590779 193596750 14.2447 11.3627
Pocillopora_meandrina_HIv1___Sc0000008 12446599 181446037 14.578 10.6047
Pocillopora_meandrina_HIv1___Sc0000009 11983232 107726980 8.9898 20.2598
Pocillopora_meandrina_HIv1___Sc0000010 11763137 156361390 13.2925 13.0258
Pocillopora_meandrina_HIv1___Sc0000011 10501528 170387591 16.225 9.48
Pocillopora_meandrina_HIv1___Sc0000012 10024633 144148537 14.3794 13.3051
Pocillopora_meandrina_HIv1___Sc0000013 9946974 103520823 10.4073 10.6624
Pocillopora_meandrina_HIv1___Sc0000014 9536826 143473871 15.0442 10.1636
Pocillopora_meandrina_HIv1___Sc0000015 9393205 129522995 13.789 10.4914
Pocillopora_meandrina_HIv1___Sc0000016 9288165 121212659 13.0502 10.6577
Pocillopora_meandrina_HIv1___Sc0000017 9274345 124783047 13.4546 10.0684
Pocillopora_meandrina_HIv1___Sc0000018 8584156 122268999 14.2436 10.0393
Pocillopora_meandrina_HIv1___Sc0000019 7112774 96996722 13.637 11.7889
Pocillopora_meandrina_HIv1___Sc0000020 6748058 100314458 14.8657 13.7742
Pocillopora_meandrina_HIv1___Sc0000021 6546105 98643507 15.069 11.1103
Pocillopora_meandrina_HIv1___Sc0000022 6319256 81331679 12.8705 14.0989
Pocillopora_meandrina_HIv1___Sc0000023 5767069 58856744 10.2057 9.9554
Pocillopora_meandrina_HIv1___Sc0000024 5762297 49631567 8.6132 10.2971
Pocillopora_meandrina_HIv1___Sc0000025 5759531 70444950 12.231 12.3173
Pocillopora_meandrina_HIv1___Sc0000026 5647578 91284572 16.1635 9.8774
Pocillopora_meandrina_HIv1___Sc0000027 5550630 68097118 12.2684 12.9673
Pocillopora_meandrina_HIv1___Sc0000028 5130920 77528196 15.11 11.1506
Pocillopora_meandrina_HIv1___Sc0000029 4860867 54539760 11.2202 10.1219
Pocillopora_meandrina_HIv1___Sc0000030 4843735 70662238 14.5884 9.7824
Pocillopora_meandrina_HIv1___Sc0000031 4691590 65005977 13.8559 10.0141
Pocillopora_meandrina_HIv1___Sc0000032 3615800 54223014 14.9961 10.3273
Pocillopora_meandrina_HIv1___Sc0000033 3306609 34714334 10.4985 10.6656
Pocillopora_meandrina_HIv1___Sc0000034 3122802 46065740 14.7514 11.0095
Pocillopora_meandrina_HIv1___Sc0000035 3015365 30849765 10.2309 10.0917
Pocillopora_meandrina_HIv1___Sc0000036 3007169 48766490 16.2167 10.074
Pocillopora_meandrina_HIv1___Sc0000037 2860435 38945662 13.6153 11.2809
Pocillopora_meandrina_HIv1___Sc0000038 2701138 33726492 12.486 12.0069
Pocillopora_meandrina_HIv1___Sc0000039 2599273 27926501 10.744 11.107
Pocillopora_meandrina_HIv1___Sc0000040 2445666 33147696 13.5536 12.8893
Pocillopora_meandrina_HIv1___Sc0000041 2159376 32799529 15.1894 10.0117
Pocillopora_meandrina_HIv1___Sc0000042 1957488 23548704 12.0301 10.6557
Pocillopora_meandrina_HIv1___Sc0000043 1845599 24132190 13.0755 10.6515
Pocillopora_meandrina_HIv1___Sc0000044 1724711 25383098 14.7173 11.144
Pocillopora_meandrina_HIv1___Sc0000045 1153740 13396498 11.6114 10.3359
Pocillopora_meandrina_HIv1___Sc0000046 755410 7389263 9.7818 16.357
Pocillopora_meandrina_HIv1___Sc0000047 239089 1051577 4.3983 6.2178
Pocillopora_meandrina_HIv1___Sc0000048 214660 69063 0.3217 1.7909
Pocillopora_meandrina_HIv1___Sc0000049 179266 146444 0.8169 2.8598
Pocillopora_meandrina_HIv1___Sc0000050 177168 304730 1.72 5.0797
Pocillopora_meandrina_HIv1___Sc0000051 165057 1373084 8.3188 11.8534
Pocillopora_meandrina_HIv1___Sc0000052 155210 67446 0.4345 4.9403
Pocillopora_meandrina_HIv1___Sc0000053 123249 285946 2.3201 6.3066
Pocillopora_meandrina_HIv1___Sc0000054 122643 1569117 12.7942 12.7108
Pocillopora_meandrina_HIv1___Sc0000055 121609 672615 5.531 9.993
Pocillopora_meandrina_HIv1___Sc0000056 112816 55827 0.4949 5.3022
Pocillopora_meandrina_HIv1___Sc0000057 107171 269833 2.5178 5.6367
Pocillopora_meandrina_HIv1___Sc0000058 98341 44999 0.4576 4.3427
Pocillopora_meandrina_HIv1___Sc0000059 83292 11479 0.1378 0.6192
Pocillopora_meandrina_HIv1___Sc0000060 79483 949 0.0119 0.1345
Pocillopora_meandrina_HIv1___Sc0000061 75390 286594 3.8015 8.6971
Pocillopora_meandrina_HIv1___Sc0000062 74194 13637 0.1838 0.8252
Pocillopora_meandrina_HIv1___Sc0000063 73457 105754 1.4397 14.6251
Pocillopora_meandrina_HIv1___Sc0000064 72700 9803 0.1348 0.6341
Pocillopora_meandrina_HIv1___Sc0000065 67986 3167 0.0466 0.6451
Pocillopora_meandrina_HIv1___Sc0000066 66659 365576 5.4843 6.337
Pocillopora_meandrina_HIv1___Sc0000067 64947 191989 2.9561 5.5679
Pocillopora_meandrina_HIv1___Sc0000068 64340 38232 0.5942 1.8329
Pocillopora_meandrina_HIv1___Sc0000069 62616 385952 6.1638 7.0618
Pocillopora_meandrina_HIv1___Sc0000070 60121 105315 1.7517 8.7995
Pocillopora_meandrina_HIv1___Sc0000071 57157 49868 0.8725 2.3181
Pocillopora_meandrina_HIv1___Sc0000072 56626 18957 0.3348 3.5411
Pocillopora_meandrina_HIv1___Sc0000073 56082 15510 0.2766 1.4536
Pocillopora_meandrina_HIv1___Sc0000074 55210 1415 0.0256 0.2017
Pocillopora_meandrina_HIv1___Sc0000075 54685 3224 0.059 0.3265
Pocillopora_meandrina_HIv1___Sc0000076 54587 195727 3.5856 18.2598
Pocillopora_meandrina_HIv1___Sc0000077 53379 31918 0.598 1.2029
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 2795 0.0563 0.2751
Pocillopora_meandrina_HIv1___Sc0000080 47218 102854 2.1783 5.3915
Pocillopora_meandrina_HIv1___Sc0000081 42490 7706 0.1814 0.6806
Pocillopora_meandrina_HIv1___Sc0000082 32657 841036 25.7536 46.3089
Pocillopora_meandrina_HIv1___Sc0000083 27992 125782 4.4935 2.7304
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 17807368 11.1184 16.9546
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3463763 2.892 5.4311
Pocillopora_meandrina_HIv1___xfSc0000002 779520 7083151 9.0866 11.4124
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1512447 3.2712 5.0078
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1145982 3.4231 5.8281
Pocillopora_meandrina_HIv1___xfSc0000006 290100 509514 1.7563 4.0152
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1031769 4.0901 6.1248
Pocillopora_meandrina_HIv1___xfSc0000012 148278 887855 5.9878 7.3275
Pocillopora_meandrina_HIv1___xfSc0000014 118081 22242 0.1884 0.7682
Pocillopora_meandrina_HIv1___xfSc0000017 98555 676187 6.861 104.8857
Pocillopora_meandrina_HIv1___xfSc0000021 95778 433350 4.5245 9.1806
Pocillopora_meandrina_HIv1___xfSc0000024 90744 698849 7.7013 12.7213
Pocillopora_meandrina_HIv1___xfSc0000029 85532 275735 3.2238 8.1022
Pocillopora_meandrina_HIv1___xfSc0000038 77395 18409 0.2379 1.2526
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1107199 15.8811 17.6353
Pocillopora_meandrina_HIv1___xfSc0000059 69426 846283 12.1897 11.5593
Pocillopora_meandrina_HIv1___xfSc0000074 66573 362033 5.4381 7.2012
Pocillopora_meandrina_HIv1___xfSc0000081 65415 495169 7.5697 6.828
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1014860 15.5375 11.9489
Pocillopora_meandrina_HIv1___xfSc0000092 63607 705868 11.0973 7.5544
Pocillopora_meandrina_HIv1___xfSc0000094 62842 173298 2.7577 5.4909
Pocillopora_meandrina_HIv1___xfSc0000113 60556 732014 12.0882 9.2492
Pocillopora_meandrina_HIv1___xfSc0000132 59032 1041005 17.6346 22.7471
Pocillopora_meandrina_HIv1___xfSc0000145 58221 227760 3.912 4.7477
Pocillopora_meandrina_HIv1___xfSc0000146 58151 340444 5.8545 7.0189
Pocillopora_meandrina_HIv1___xfSc0000168 56681 353720 6.2405 7.6611
Pocillopora_meandrina_HIv1___xfSc0000175 56271 227640 4.0454 9.3416
Pocillopora_meandrina_HIv1___xfSc0000195 55223 94872 1.718 3.1992
Pocillopora_meandrina_HIv1___xfSc0000199 55095 320739 5.8216 10.4443
Pocillopora_meandrina_HIv1___xfSc0000205 54658 275110 5.0333 5.902
Pocillopora_meandrina_HIv1___xfSc0000206 54623 242791 4.4448 6.8099
Pocillopora_meandrina_HIv1___xfSc0000212 54299 311552 5.7377 9.445
Pocillopora_meandrina_HIv1___xfSc0000217 54168 390615 7.2112 15.5551
Pocillopora_meandrina_HIv1___xfSc0000223 53823 285207 5.299 6.2502
Pocillopora_meandrina_HIv1___xfSc0000228 53382 380814 7.1338 21.093
Pocillopora_meandrina_HIv1___xfSc0000237 53049 374444 7.0585 7.8917
Pocillopora_meandrina_HIv1___xfSc0000262 52308 352884 6.7463 7.4636
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2720985 52.0623 49.4534
Pocillopora_meandrina_HIv1___xfSc0000272 52107 465014 8.9242 10.6437
Pocillopora_meandrina_HIv1___xfSc0000275 51938 498777 9.6033 9.9818
Pocillopora_meandrina_HIv1___xfSc0000284 51483 337845 6.5623 8.7323
Pocillopora_meandrina_HIv1___xfSc0000288 51367 607900 11.8344 11.4769
Pocillopora_meandrina_HIv1___xfSc0000300 50845 11455 0.2253 0.8468
Pocillopora_meandrina_HIv1___xfSc0000301 50809 402952 7.9307 8.9902
Pocillopora_meandrina_HIv1___xfSc0000343 49544 190941 3.854 7.0991
Pocillopora_meandrina_HIv1___xfSc0000376 48519 415231 8.5581 22.3153
Pocillopora_meandrina_HIv1___xfSc0000415 47398 235048 4.959 5.8682
Pocillopora_meandrina_HIv1___xfSc0000423 47202 61315 1.299 3.043
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1207202 25.6328 21.4238
Pocillopora_meandrina_HIv1___xfSc0000428 47057 223198 4.7431 9.0422
Pocillopora_meandrina_HIv1___xfSc0000436 46816 399547 8.5344 12.0149
Pocillopora_meandrina_HIv1___xfSc0000445 46561 357400 7.676 7.1222
Pocillopora_meandrina_HIv1___xfSc0000447 46542 567665 12.1968 10.8695
Pocillopora_meandrina_HIv1___xfSc0000469 45938 454262 9.8886 7.1794
Pocillopora_meandrina_HIv1___xfSc0000477 45781 153389 3.3505 5.61
Pocillopora_meandrina_HIv1___xfSc0000479 45736 152968 3.3446 5.2809
Pocillopora_meandrina_HIv1___xfSc0000482 45585 584669 12.8259 17.2266
Pocillopora_meandrina_HIv1___xfSc0000488 45379 97529 2.1492 4.0936
Pocillopora_meandrina_HIv1___xfSc0000506 44781 290488 6.4869 8.0574
Pocillopora_meandrina_HIv1___xfSc0000527 44235 263933 5.9666 6.8204
Pocillopora_meandrina_HIv1___xfSc0000540 43935 334475 7.613 9.7274
Pocillopora_meandrina_HIv1___xfSc0000555 43535 289016 6.6387 10.9595
Pocillopora_meandrina_HIv1___xfSc0000565 43357 253934 5.8568 5.5609
Pocillopora_meandrina_HIv1___xfSc0000566 43316 288936 6.6704 8.5283
Pocillopora_meandrina_HIv1___xfSc0000567 43305 181817 4.1985 7.8053
Pocillopora_meandrina_HIv1___xfSc0000570 43295 159967 3.6948 5.3633
Pocillopora_meandrina_HIv1___xfSc0000579 43029 74142 1.7231 3.7971
Pocillopora_meandrina_HIv1___xfSc0000583 42958 251793 5.8614 6.0343
Pocillopora_meandrina_HIv1___xfSc0000596 42675 193667 4.5382 6.833
Pocillopora_meandrina_HIv1___xfSc0000612 42423 239022 5.6343 5.3764
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2680364 63.2833 221.8377
Pocillopora_meandrina_HIv1___xfSc0000621 42164 376395 8.9269 9.1209
Pocillopora_meandrina_HIv1___xfSc0000642 41754 355887 8.5234 11.3799
Pocillopora_meandrina_HIv1___xfSc0000655 41446 542297 13.0844 26.7214
Pocillopora_meandrina_HIv1___xfSc0000692 40426 62113 1.5365 4.7003
Pocillopora_meandrina_HIv1___xfSc0000699 40296 28928 0.7179 2.0247
Pocillopora_meandrina_HIv1___xfSc0000704 40233 152589 3.7926 7.2556
Pocillopora_meandrina_HIv1___xfSc0000705 40197 163687 4.0721 5.3095
Pocillopora_meandrina_HIv1___xfSc0000716 39998 332784 8.32 8.5116
Pocillopora_meandrina_HIv1___xfSc0000725 39827 232834 5.8461 13.4756
Pocillopora_meandrina_HIv1___xfSc0000729 39775 21017 0.5284 3.2895
Pocillopora_meandrina_HIv1___xfSc0000760 39228 19062 0.4859 1.224
Pocillopora_meandrina_HIv1___xfSc0000763 39151 332464 8.4918 6.6083
Pocillopora_meandrina_HIv1___xfSc0000765 39117 126958 3.2456 6.3971
Pocillopora_meandrina_HIv1___xfSc0000788 38513 392389 10.1885 8.8307
Pocillopora_meandrina_HIv1___xfSc0000811 37888 613808 16.2006 10.5249
Pocillopora_meandrina_HIv1___xfSc0000812 37881 28260 0.746 1.9884
Pocillopora_meandrina_HIv1___xfSc0000817 37779 398996 10.5613 8.2561
Pocillopora_meandrina_HIv1___xfSc0000824 37656 102514 2.7224 4.9048
Pocillopora_meandrina_HIv1___xfSc0000835 37434 318144 8.4988 10.8167
Pocillopora_meandrina_HIv1___xfSc0000836 37372 216873 5.8031 8.7637
Pocillopora_meandrina_HIv1___xfSc0000837 37368 277526 7.4268 9.0677
Pocillopora_meandrina_HIv1___xfSc0000840 37283 248682 6.6701 10.473
Pocillopora_meandrina_HIv1___xfSc0000857 37006 123795 3.3453 4.4192
Pocillopora_meandrina_HIv1___xfSc0000859 36995 106940 2.8907 6.5117
Pocillopora_meandrina_HIv1___xfSc0000866 36925 122730 3.3238 5.531
Pocillopora_meandrina_HIv1___xfSc0000868 36831 128671 3.4936 7.6161
Pocillopora_meandrina_HIv1___xfSc0000875 36611 43605 1.191 3.0459
Pocillopora_meandrina_HIv1___xfSc0000885 36416 183110 5.0283 6.5816
Pocillopora_meandrina_HIv1___xfSc0000886 36355 45960 1.2642 3.7302
Pocillopora_meandrina_HIv1___xfSc0000890 36339 237607 6.5386 9.0954
Pocillopora_meandrina_HIv1___xfSc0000892 36267 59072 1.6288 6.3444
Pocillopora_meandrina_HIv1___xfSc0000943 35168 8523 0.2424 1.1024
Pocillopora_meandrina_HIv1___xfSc0000948 35100 323352 9.2123 11.2104
Pocillopora_meandrina_HIv1___xfSc0000952 34934 207496 5.9397 6.273
Pocillopora_meandrina_HIv1___xfSc0000953 34905 117673 3.3712 4.7372
Pocillopora_meandrina_HIv1___xfSc0000957 34773 121823 3.5034 7.1445
Pocillopora_meandrina_HIv1___xfSc0000968 34345 60206 1.753 4.5644
Pocillopora_meandrina_HIv1___xfSc0000974 34140 292625 8.5713 6.9938
Pocillopora_meandrina_HIv1___xfSc0000975 33988 391495 11.5186 13.4384
Pocillopora_meandrina_HIv1___xfSc0000995 33324 135555 4.0678 7.4707
Pocillopora_meandrina_HIv1___xfSc0001011 32918 519078 15.7688 16.3855
Pocillopora_meandrina_HIv1___xfSc0001122 29140 314682 10.799 8.3755
Pocillopora_meandrina_HIv1___xfSc0001170 27381 69818 2.5499 5.8742
Pocillopora_meandrina_HIv1___xfSc0001179 27200 87505 3.2171 4.6194
Pocillopora_meandrina_HIv1___xfSc0001231 22938 14543 0.634 1.1101
Pocillopora_meandrina_HIv1___xfSc0001237 22715 94833 4.1749 10.4995
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1276997 3.1278 5.7984
Pocillopora_meandrina_HIv1___xpSc0001275 48561 158904 3.2723 6.4596
Pocillopora_meandrina_HIv1___xpSc0001276 38618 49770 1.2888 3.1979
Pocillopora_meandrina_HIv1___xpSc0001280 35955 96670 2.6886 5.1523
Pocillopora_meandrina_HIv1___xpSc0001281 34238 219125 6.4001 8.3251
Pocillopora_meandrina_HIv1___xpSc0001290 28931 322094 11.1332 8.7143
Pocillopora_meandrina_HIv1___xpSc0001321 15304 90706 5.9269 10.2622
Pocillopora_meandrina_HIv1___xpSc0001331 8958 168423 18.8014 9.5974
Pocillopora_meandrina_HIv1___xpSc0001337 6786 21601 3.1832 7.0337
Pocillopora_meandrina_HIv1___xpSc0001344 5647 45012 7.971 10.8368
Pocillopora_meandrina_HIv1___xpSc0001355 3576 52980 14.8154 8.5791

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 20:32:26
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