Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-52-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-52-TP2_R1_001.fastp-trim.fq.gz -2 POC-52-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-52-TP2 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:46:41 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-52-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 44,719,290
Mapped reads 44,719,290 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 44,719,290 / 100%
Mapped reads, first in pair 22,359,645 / 50%
Mapped reads, second in pair 22,359,645 / 50%
Mapped reads, both in pair 44,719,290 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 132.89
Overlapping read pairs 15,980,830 / 71.47%
Duplicated reads (estimated) 4,628,872 / 10.35%
Duplication rate 10.16%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,385,173,025 / 40.31%
Number/percentage of C's 576,311,640 / 9.74%
Number/percentage of T's 2,390,605,380 / 40.41%
Number/percentage of G's 563,795,626 / 9.53%
Number/percentage of N's 487,849 / 0.01%
GC Percentage 19.27%

Coverage

Mean 15.7612
Standard Deviation 14.1322
Mean (paired-end reads overlap ignored) 12.54

Mapping Quality

Mean Mapping Quality 22.46

Insert size

Mean 231.17
Standard Deviation 82.11
P25/Median/P75 166 / 214 / 280

Mismatches and indels

General error rate 21.14%
Mismatches 1,228,635,223
Insertions 8,815,266
Mapped reads with at least one insertion 14.8%
Deletions 7,022,735
Mapped reads with at least one deletion 13.17%
Homopolymer indels 52.11%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 358331123 16.5502 12.0789
Pocillopora_meandrina_HIv1___Sc0000001 21507942 381987915 17.7603 12.3288
Pocillopora_meandrina_HIv1___Sc0000002 19741974 347867300 17.6207 12.0344
Pocillopora_meandrina_HIv1___Sc0000003 19417450 301595957 15.5322 13.9834
Pocillopora_meandrina_HIv1___Sc0000004 14584444 224893237 15.4201 22.2765
Pocillopora_meandrina_HIv1___Sc0000005 14098929 237038520 16.8125 11.2862
Pocillopora_meandrina_HIv1___Sc0000006 14068054 235546266 16.7433 13.7153
Pocillopora_meandrina_HIv1___Sc0000007 13590779 224939988 16.5509 13.1198
Pocillopora_meandrina_HIv1___Sc0000008 12446599 224689679 18.0523 12.6722
Pocillopora_meandrina_HIv1___Sc0000009 11983232 143127598 11.944 19.5395
Pocillopora_meandrina_HIv1___Sc0000010 11763137 184469812 15.682 14.4243
Pocillopora_meandrina_HIv1___Sc0000011 10501528 204648708 19.4875 11.6777
Pocillopora_meandrina_HIv1___Sc0000012 10024633 163804600 16.3402 13.9231
Pocillopora_meandrina_HIv1___Sc0000013 9946974 124701602 12.5366 12.5888
Pocillopora_meandrina_HIv1___Sc0000014 9536826 171624455 17.996 11.9954
Pocillopora_meandrina_HIv1___Sc0000015 9393205 150753704 16.0492 11.8148
Pocillopora_meandrina_HIv1___Sc0000016 9288165 144486459 15.556 11.9562
Pocillopora_meandrina_HIv1___Sc0000017 9274345 149076744 16.0741 12.1529
Pocillopora_meandrina_HIv1___Sc0000018 8584156 144397082 16.8213 11.5417
Pocillopora_meandrina_HIv1___Sc0000019 7112774 117013077 16.4511 13.2027
Pocillopora_meandrina_HIv1___Sc0000020 6748058 115781145 17.1577 15.7576
Pocillopora_meandrina_HIv1___Sc0000021 6546105 115309984 17.6151 11.8407
Pocillopora_meandrina_HIv1___Sc0000022 6319256 94218090 14.9097 14.9745
Pocillopora_meandrina_HIv1___Sc0000023 5767069 80126564 13.8938 12.7009
Pocillopora_meandrina_HIv1___Sc0000024 5762297 62546468 10.8544 13.0801
Pocillopora_meandrina_HIv1___Sc0000025 5759531 84540592 14.6784 14.3126
Pocillopora_meandrina_HIv1___Sc0000026 5647578 108130699 19.1464 11.6777
Pocillopora_meandrina_HIv1___Sc0000027 5550630 82273016 14.8223 18.0952
Pocillopora_meandrina_HIv1___Sc0000028 5130920 91532516 17.8394 13.5786
Pocillopora_meandrina_HIv1___Sc0000029 4860867 65122831 13.3974 12.7203
Pocillopora_meandrina_HIv1___Sc0000030 4843735 85807869 17.7152 12.4782
Pocillopora_meandrina_HIv1___Sc0000031 4691590 78943146 16.8265 12.1891
Pocillopora_meandrina_HIv1___Sc0000032 3615800 65876713 18.2191 14.0957
Pocillopora_meandrina_HIv1___Sc0000033 3306609 43446176 13.1392 13.5256
Pocillopora_meandrina_HIv1___Sc0000034 3122802 54025562 17.3003 12.1112
Pocillopora_meandrina_HIv1___Sc0000035 3015365 38529565 12.7777 16.4344
Pocillopora_meandrina_HIv1___Sc0000036 3007169 62201131 20.6843 12.0885
Pocillopora_meandrina_HIv1___Sc0000037 2860435 45439406 15.8855 13.3388
Pocillopora_meandrina_HIv1___Sc0000038 2701138 40474588 14.9843 14.2761
Pocillopora_meandrina_HIv1___Sc0000039 2599273 33989892 13.0767 15.2202
Pocillopora_meandrina_HIv1___Sc0000040 2445666 35181305 14.3852 13.756
Pocillopora_meandrina_HIv1___Sc0000041 2159376 37885878 17.5448 13.2128
Pocillopora_meandrina_HIv1___Sc0000042 1957488 29762675 15.2045 12.306
Pocillopora_meandrina_HIv1___Sc0000043 1845599 25583937 13.8621 11.5732
Pocillopora_meandrina_HIv1___Sc0000044 1724711 29801025 17.2789 12.3715
Pocillopora_meandrina_HIv1___Sc0000045 1153740 15291652 13.254 12.2487
Pocillopora_meandrina_HIv1___Sc0000046 755410 8445777 11.1804 13.7798
Pocillopora_meandrina_HIv1___Sc0000047 239089 146824 0.6141 2.3124
Pocillopora_meandrina_HIv1___Sc0000048 214660 39691 0.1849 1.2523
Pocillopora_meandrina_HIv1___Sc0000049 179266 751179 4.1903 9.5102
Pocillopora_meandrina_HIv1___Sc0000050 177168 167482 0.9453 2.4153
Pocillopora_meandrina_HIv1___Sc0000051 165057 876068 5.3077 9.4418
Pocillopora_meandrina_HIv1___Sc0000052 155210 23783 0.1532 1.4718
Pocillopora_meandrina_HIv1___Sc0000053 123249 222456 1.8049 5.9499
Pocillopora_meandrina_HIv1___Sc0000054 122643 1925267 15.6981 25.3444
Pocillopora_meandrina_HIv1___Sc0000055 121609 530115 4.3592 9.7475
Pocillopora_meandrina_HIv1___Sc0000056 112816 52343 0.464 4.754
Pocillopora_meandrina_HIv1___Sc0000057 107171 473352 4.4168 10.1689
Pocillopora_meandrina_HIv1___Sc0000058 98341 31555 0.3209 3.7364
Pocillopora_meandrina_HIv1___Sc0000059 83292 1348 0.0162 0.2053
Pocillopora_meandrina_HIv1___Sc0000060 79483 0 0 0
Pocillopora_meandrina_HIv1___Sc0000061 75390 391243 5.1896 11.8424
Pocillopora_meandrina_HIv1___Sc0000062 74194 12004 0.1618 0.7553
Pocillopora_meandrina_HIv1___Sc0000063 73457 46239 0.6295 6.5266
Pocillopora_meandrina_HIv1___Sc0000064 72700 5251 0.0722 0.4373
Pocillopora_meandrina_HIv1___Sc0000065 67986 2867 0.0422 0.3786
Pocillopora_meandrina_HIv1___Sc0000066 66659 476694 7.1512 7.749
Pocillopora_meandrina_HIv1___Sc0000067 64947 152691 2.351 4.7004
Pocillopora_meandrina_HIv1___Sc0000068 64340 7670 0.1192 0.7381
Pocillopora_meandrina_HIv1___Sc0000069 62616 172218 2.7504 7.3267
Pocillopora_meandrina_HIv1___Sc0000070 60121 42113 0.7005 3.1183
Pocillopora_meandrina_HIv1___Sc0000071 57157 35939 0.6288 1.633
Pocillopora_meandrina_HIv1___Sc0000072 56626 11826 0.2088 2.3905
Pocillopora_meandrina_HIv1___Sc0000073 56082 13720 0.2446 0.896
Pocillopora_meandrina_HIv1___Sc0000074 55210 489 0.0089 0.1287
Pocillopora_meandrina_HIv1___Sc0000075 54685 800 0.0146 0.137
Pocillopora_meandrina_HIv1___Sc0000076 54587 174532 3.1973 16.0678
Pocillopora_meandrina_HIv1___Sc0000077 53379 15920 0.2982 0.8647
Pocillopora_meandrina_HIv1___Sc0000078 51564 540 0.0105 0.1203
Pocillopora_meandrina_HIv1___Sc0000079 49664 664 0.0134 0.13
Pocillopora_meandrina_HIv1___Sc0000080 47218 90181 1.9099 4.9343
Pocillopora_meandrina_HIv1___Sc0000081 42490 11670 0.2747 0.8145
Pocillopora_meandrina_HIv1___Sc0000082 32657 601317 18.4131 41.954
Pocillopora_meandrina_HIv1___Sc0000083 27992 2605 0.0931 0.5833
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 12235252 7.6394 13.3118
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 4344889 3.6276 7.602
Pocillopora_meandrina_HIv1___xfSc0000002 779520 6164966 7.9087 10.3739
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1640965 3.5492 7.4411
Pocillopora_meandrina_HIv1___xfSc0000004 334777 752712 2.2484 4.7203
Pocillopora_meandrina_HIv1___xfSc0000006 290100 588479 2.0285 4.1885
Pocillopora_meandrina_HIv1___xfSc0000007 252258 669915 2.6557 4.9161
Pocillopora_meandrina_HIv1___xfSc0000012 148278 487173 3.2855 6.8058
Pocillopora_meandrina_HIv1___xfSc0000014 118081 28740 0.2434 0.9705
Pocillopora_meandrina_HIv1___xfSc0000017 98555 629717 6.3895 100.57
Pocillopora_meandrina_HIv1___xfSc0000021 95778 619066 6.4636 11.7007
Pocillopora_meandrina_HIv1___xfSc0000024 90744 607797 6.6979 9.8966
Pocillopora_meandrina_HIv1___xfSc0000029 85532 108527 1.2688 5.1609
Pocillopora_meandrina_HIv1___xfSc0000038 77395 80428 1.0392 11.6574
Pocillopora_meandrina_HIv1___xfSc0000058 69718 564649 8.099 12.3892
Pocillopora_meandrina_HIv1___xfSc0000059 69426 296325 4.2682 8.8727
Pocillopora_meandrina_HIv1___xfSc0000074 66573 526896 7.9146 9.4751
Pocillopora_meandrina_HIv1___xfSc0000081 65415 489407 7.4816 9.2931
Pocillopora_meandrina_HIv1___xfSc0000083 65317 898258 13.7523 14.3647
Pocillopora_meandrina_HIv1___xfSc0000092 63607 553738 8.7056 9.8616
Pocillopora_meandrina_HIv1___xfSc0000094 62842 60976 0.9703 2.6129
Pocillopora_meandrina_HIv1___xfSc0000113 60556 872895 14.4147 16.4748
Pocillopora_meandrina_HIv1___xfSc0000132 59032 47950 0.8123 2.1736
Pocillopora_meandrina_HIv1___xfSc0000145 58221 287041 4.9302 6.1946
Pocillopora_meandrina_HIv1___xfSc0000146 58151 148018 2.5454 6.0511
Pocillopora_meandrina_HIv1___xfSc0000168 56681 336455 5.9359 9.1079
Pocillopora_meandrina_HIv1___xfSc0000175 56271 246352 4.378 11.6825
Pocillopora_meandrina_HIv1___xfSc0000195 55223 15627 0.283 2.304
Pocillopora_meandrina_HIv1___xfSc0000199 55095 459998 8.3492 17.4353
Pocillopora_meandrina_HIv1___xfSc0000205 54658 62607 1.1454 2.577
Pocillopora_meandrina_HIv1___xfSc0000206 54623 198408 3.6323 5.7774
Pocillopora_meandrina_HIv1___xfSc0000212 54299 321678 5.9242 8.4583
Pocillopora_meandrina_HIv1___xfSc0000217 54168 327659 6.0489 10.6623
Pocillopora_meandrina_HIv1___xfSc0000223 53823 553696 10.2873 9.28
Pocillopora_meandrina_HIv1___xfSc0000228 53382 484080 9.0682 28.4968
Pocillopora_meandrina_HIv1___xfSc0000237 53049 253613 4.7807 7.5652
Pocillopora_meandrina_HIv1___xfSc0000262 52308 260294 4.9762 7.1987
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1820865 34.8398 29.2239
Pocillopora_meandrina_HIv1___xfSc0000272 52107 269756 5.177 8.4669
Pocillopora_meandrina_HIv1___xfSc0000275 51938 455608 8.7722 10.8062
Pocillopora_meandrina_HIv1___xfSc0000284 51483 495237 9.6194 12.2818
Pocillopora_meandrina_HIv1___xfSc0000288 51367 289030 5.6268 12.8892
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9995 0.1966 0.8208
Pocillopora_meandrina_HIv1___xfSc0000301 50809 562892 11.0786 10.8065
Pocillopora_meandrina_HIv1___xfSc0000343 49544 175052 3.5333 7.1072
Pocillopora_meandrina_HIv1___xfSc0000376 48519 458843 9.457 30.6474
Pocillopora_meandrina_HIv1___xfSc0000415 47398 280440 5.9167 7.2756
Pocillopora_meandrina_HIv1___xfSc0000423 47202 67527 1.4306 4.3051
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1056485 22.4326 24.3616
Pocillopora_meandrina_HIv1___xfSc0000428 47057 614054 13.0492 19.1591
Pocillopora_meandrina_HIv1___xfSc0000436 46816 302912 6.4703 15.1363
Pocillopora_meandrina_HIv1___xfSc0000445 46561 57523 1.2354 2.9016
Pocillopora_meandrina_HIv1___xfSc0000447 46542 432911 9.3015 13.6068
Pocillopora_meandrina_HIv1___xfSc0000469 45938 354034 7.7068 7.6597
Pocillopora_meandrina_HIv1___xfSc0000477 45781 300714 6.5685 7.4397
Pocillopora_meandrina_HIv1___xfSc0000479 45736 163907 3.5838 5.8097
Pocillopora_meandrina_HIv1___xfSc0000482 45585 518141 11.3665 20.5014
Pocillopora_meandrina_HIv1___xfSc0000488 45379 209924 4.626 6.9499
Pocillopora_meandrina_HIv1___xfSc0000506 44781 156768 3.5008 5.8209
Pocillopora_meandrina_HIv1___xfSc0000527 44235 213133 4.8182 7.4218
Pocillopora_meandrina_HIv1___xfSc0000540 43935 344861 7.8493 11.3178
Pocillopora_meandrina_HIv1___xfSc0000555 43535 240032 5.5135 12.288
Pocillopora_meandrina_HIv1___xfSc0000565 43357 376867 8.6922 8.886
Pocillopora_meandrina_HIv1___xfSc0000566 43316 235292 5.432 9.1977
Pocillopora_meandrina_HIv1___xfSc0000567 43305 190384 4.3964 8.9753
Pocillopora_meandrina_HIv1___xfSc0000570 43295 107508 2.4832 6.4888
Pocillopora_meandrina_HIv1___xfSc0000579 43029 67105 1.5595 4.0721
Pocillopora_meandrina_HIv1___xfSc0000583 42958 307209 7.1514 8.1813
Pocillopora_meandrina_HIv1___xfSc0000596 42675 116838 2.7379 5.2149
Pocillopora_meandrina_HIv1___xfSc0000612 42423 167458 3.9473 6.1283
Pocillopora_meandrina_HIv1___xfSc0000616 42355 2581955 60.9599 162.3919
Pocillopora_meandrina_HIv1___xfSc0000621 42164 284425 6.7457 8.0361
Pocillopora_meandrina_HIv1___xfSc0000642 41754 192471 4.6096 7.2641
Pocillopora_meandrina_HIv1___xfSc0000655 41446 530288 12.7947 26.003
Pocillopora_meandrina_HIv1___xfSc0000692 40426 118841 2.9397 4.9107
Pocillopora_meandrina_HIv1___xfSc0000699 40296 40626 1.0082 2.337
Pocillopora_meandrina_HIv1___xfSc0000704 40233 559438 13.905 18.9984
Pocillopora_meandrina_HIv1___xfSc0000705 40197 101856 2.5339 5.5006
Pocillopora_meandrina_HIv1___xfSc0000716 39998 328474 8.2123 9.3877
Pocillopora_meandrina_HIv1___xfSc0000725 39827 60373 1.5159 5.6326
Pocillopora_meandrina_HIv1___xfSc0000729 39775 88886 2.2347 19.9103
Pocillopora_meandrina_HIv1___xfSc0000760 39228 18552 0.4729 2.147
Pocillopora_meandrina_HIv1___xfSc0000763 39151 261111 6.6693 7.0177
Pocillopora_meandrina_HIv1___xfSc0000765 39117 70947 1.8137 4.0519
Pocillopora_meandrina_HIv1___xfSc0000788 38513 267083 6.9349 9.3624
Pocillopora_meandrina_HIv1___xfSc0000811 37888 226162 5.9692 5.7669
Pocillopora_meandrina_HIv1___xfSc0000812 37881 14047 0.3708 0.9316
Pocillopora_meandrina_HIv1___xfSc0000817 37779 424346 11.2323 9.4276
Pocillopora_meandrina_HIv1___xfSc0000824 37656 208602 5.5397 7.1294
Pocillopora_meandrina_HIv1___xfSc0000835 37434 292674 7.8184 9.419
Pocillopora_meandrina_HIv1___xfSc0000836 37372 205835 5.5077 8.9827
Pocillopora_meandrina_HIv1___xfSc0000837 37368 146142 3.9109 7.5438
Pocillopora_meandrina_HIv1___xfSc0000840 37283 415368 11.1409 20.0564
Pocillopora_meandrina_HIv1___xfSc0000857 37006 64429 1.741 3.8666
Pocillopora_meandrina_HIv1___xfSc0000859 36995 49319 1.3331 2.3588
Pocillopora_meandrina_HIv1___xfSc0000866 36925 89707 2.4294 5.1114
Pocillopora_meandrina_HIv1___xfSc0000868 36831 136443 3.7046 8.2846
Pocillopora_meandrina_HIv1___xfSc0000875 36611 17510 0.4783 1.581
Pocillopora_meandrina_HIv1___xfSc0000885 36416 153216 4.2074 6.5848
Pocillopora_meandrina_HIv1___xfSc0000886 36355 268565 7.3873 11.9444
Pocillopora_meandrina_HIv1___xfSc0000890 36339 186558 5.1338 13.544
Pocillopora_meandrina_HIv1___xfSc0000892 36267 29173 0.8044 2.6129
Pocillopora_meandrina_HIv1___xfSc0000943 35168 8027 0.2282 1.2574
Pocillopora_meandrina_HIv1___xfSc0000948 35100 223764 6.375 8.5815
Pocillopora_meandrina_HIv1___xfSc0000952 34934 91278 2.6129 5.2711
Pocillopora_meandrina_HIv1___xfSc0000953 34905 172925 4.9542 6.2846
Pocillopora_meandrina_HIv1___xfSc0000957 34773 253770 7.2979 12.4986
Pocillopora_meandrina_HIv1___xfSc0000968 34345 15751 0.4586 1.799
Pocillopora_meandrina_HIv1___xfSc0000974 34140 241941 7.0867 7.8297
Pocillopora_meandrina_HIv1___xfSc0000975 33988 415378 12.2213 12.7892
Pocillopora_meandrina_HIv1___xfSc0000995 33324 102975 3.0901 7.4073
Pocillopora_meandrina_HIv1___xfSc0001011 32918 141916 4.3112 8.6283
Pocillopora_meandrina_HIv1___xfSc0001122 29140 280925 9.6405 12.5953
Pocillopora_meandrina_HIv1___xfSc0001170 27381 22169 0.8096 2.587
Pocillopora_meandrina_HIv1___xfSc0001179 27200 85896 3.1579 5.0578
Pocillopora_meandrina_HIv1___xfSc0001231 22938 15614 0.6807 1.2858
Pocillopora_meandrina_HIv1___xfSc0001237 22715 52984 2.3326 6.1373
Pocillopora_meandrina_HIv1___xpSc0001273 408270 2173486 5.3236 9.874
Pocillopora_meandrina_HIv1___xpSc0001275 48561 245181 5.0489 9.0037
Pocillopora_meandrina_HIv1___xpSc0001276 38618 105375 2.7286 6.5337
Pocillopora_meandrina_HIv1___xpSc0001280 35955 195997 5.4512 8.1616
Pocillopora_meandrina_HIv1___xpSc0001281 34238 191075 5.5808 9.2457
Pocillopora_meandrina_HIv1___xpSc0001290 28931 234180 8.0944 9.8823
Pocillopora_meandrina_HIv1___xpSc0001321 15304 32770 2.1413 4.5481
Pocillopora_meandrina_HIv1___xpSc0001331 8958 97307 10.8626 12.1513
Pocillopora_meandrina_HIv1___xpSc0001337 6786 9354 1.3784 3.3893
Pocillopora_meandrina_HIv1___xpSc0001344 5647 40327 7.1413 9.4468
Pocillopora_meandrina_HIv1___xpSc0001355 3576 41013 11.469 9.6121

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 20:46:43
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