Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-219-TP2.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-219-TP2_R1_001.fastp-trim.fq.gz -2 POC-219-TP2_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-219-TP2 --multicore 3"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Wed Apr 23 02:06:20 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-219-TP2.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 65,510,074
Mapped reads 65,510,074 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 65,510,074 / 100%
Mapped reads, first in pair 32,755,037 / 50%
Mapped reads, second in pair 32,755,037 / 50%
Mapped reads, both in pair 65,510,074 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 131.26
Overlapping read pairs 21,382,647 / 65.28%
Duplicated reads (estimated) 11,501,285 / 17.56%
Duplication rate 16.5%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 3,454,415,494 / 40.35%
Number/percentage of C's 833,292,062 / 9.73%
Number/percentage of T's 3,455,267,102 / 40.36%
Number/percentage of G's 817,562,386 / 9.55%
Number/percentage of N's 713,618 / 0.01%
GC Percentage 19.28%

Coverage

Mean 22.8073
Standard Deviation 21.7725
Mean (paired-end reads overlap ignored) 18.89

Mapping Quality

Mean Mapping Quality 22.69

Insert size

Mean 240.38
Standard Deviation 85.64
P25/Median/P75 174 / 233 / 295

Mismatches and indels

General error rate 21.03%
Mismatches 1,768,805,874
Insertions 12,713,986
Mapped reads with at least one insertion 14.69%
Deletions 10,277,544
Mapped reads with at least one deletion 13.16%
Homopolymer indels 52.45%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 531652423 24.5554 18.3047
Pocillopora_meandrina_HIv1___Sc0000001 21507942 557495097 25.9204 17.7453
Pocillopora_meandrina_HIv1___Sc0000002 19741974 499303392 25.2915 16.9875
Pocillopora_meandrina_HIv1___Sc0000003 19417450 435220622 22.4139 19.8337
Pocillopora_meandrina_HIv1___Sc0000004 14584444 327790418 22.4753 34.9595
Pocillopora_meandrina_HIv1___Sc0000005 14098929 347043223 24.6149 16.3873
Pocillopora_meandrina_HIv1___Sc0000006 14068054 344162246 24.4641 19.3964
Pocillopora_meandrina_HIv1___Sc0000007 13590779 328183415 24.1475 18.5644
Pocillopora_meandrina_HIv1___Sc0000008 12446599 317907849 25.5417 17.2243
Pocillopora_meandrina_HIv1___Sc0000009 11983232 178962668 14.9344 29.4454
Pocillopora_meandrina_HIv1___Sc0000010 11763137 266038818 22.6163 20.8108
Pocillopora_meandrina_HIv1___Sc0000011 10501528 296311207 28.216 15.3754
Pocillopora_meandrina_HIv1___Sc0000012 10024633 241847644 24.1253 23.1801
Pocillopora_meandrina_HIv1___Sc0000013 9946974 173140976 17.4064 17.7714
Pocillopora_meandrina_HIv1___Sc0000014 9536826 250634666 26.2807 16.745
Pocillopora_meandrina_HIv1___Sc0000015 9393205 224965222 23.9498 17.2342
Pocillopora_meandrina_HIv1___Sc0000016 9288165 209595285 22.5658 17.6072
Pocillopora_meandrina_HIv1___Sc0000017 9274345 215297200 23.2143 16.5007
Pocillopora_meandrina_HIv1___Sc0000018 8584156 210549110 24.5276 16.5024
Pocillopora_meandrina_HIv1___Sc0000019 7112774 166509135 23.4099 18.7041
Pocillopora_meandrina_HIv1___Sc0000020 6748058 172411415 25.5498 22.8224
Pocillopora_meandrina_HIv1___Sc0000021 6546105 172364455 26.3308 18.606
Pocillopora_meandrina_HIv1___Sc0000022 6319256 137809564 21.8079 23.2967
Pocillopora_meandrina_HIv1___Sc0000023 5767069 102870633 17.8376 16.7821
Pocillopora_meandrina_HIv1___Sc0000024 5762297 83699463 14.5254 17.4884
Pocillopora_meandrina_HIv1___Sc0000025 5759531 120738405 20.9632 20.8698
Pocillopora_meandrina_HIv1___Sc0000026 5647578 158453925 28.057 15.9608
Pocillopora_meandrina_HIv1___Sc0000027 5550630 115570636 20.8212 21.4971
Pocillopora_meandrina_HIv1___Sc0000028 5130920 133893911 26.0955 18.664
Pocillopora_meandrina_HIv1___Sc0000029 4860867 95044509 19.553 17.0389
Pocillopora_meandrina_HIv1___Sc0000030 4843735 123597954 25.5171 15.9583
Pocillopora_meandrina_HIv1___Sc0000031 4691590 114254120 24.353 16.4827
Pocillopora_meandrina_HIv1___Sc0000032 3615800 93538253 25.8693 17.293
Pocillopora_meandrina_HIv1___Sc0000033 3306609 60320757 18.2425 17.5654
Pocillopora_meandrina_HIv1___Sc0000034 3122802 78784205 25.2287 18.2449
Pocillopora_meandrina_HIv1___Sc0000035 3015365 52986385 17.5721 16.9733
Pocillopora_meandrina_HIv1___Sc0000036 3007169 86374561 28.7229 16.7871
Pocillopora_meandrina_HIv1___Sc0000037 2860435 67661832 23.6544 18.1096
Pocillopora_meandrina_HIv1___Sc0000038 2701138 56725083 21.0004 18.4203
Pocillopora_meandrina_HIv1___Sc0000039 2599273 47688124 18.3467 18.5539
Pocillopora_meandrina_HIv1___Sc0000040 2445666 57408755 23.4737 21.9702
Pocillopora_meandrina_HIv1___Sc0000041 2159376 56072072 25.9668 16.2602
Pocillopora_meandrina_HIv1___Sc0000042 1957488 40926206 20.9075 17.6177
Pocillopora_meandrina_HIv1___Sc0000043 1845599 41978565 22.7452 18.4379
Pocillopora_meandrina_HIv1___Sc0000044 1724711 43611900 25.2865 18.3869
Pocillopora_meandrina_HIv1___Sc0000045 1153740 22975575 19.914 17.183
Pocillopora_meandrina_HIv1___Sc0000046 755410 12661683 16.7613 31.207
Pocillopora_meandrina_HIv1___Sc0000047 239089 261230 1.0926 3.2232
Pocillopora_meandrina_HIv1___Sc0000048 214660 68336 0.3183 2.0646
Pocillopora_meandrina_HIv1___Sc0000049 179266 230772 1.2873 4.468
Pocillopora_meandrina_HIv1___Sc0000050 177168 395869 2.2344 7.2782
Pocillopora_meandrina_HIv1___Sc0000051 165057 2134927 12.9345 20.6624
Pocillopora_meandrina_HIv1___Sc0000052 155210 131646 0.8482 9.8949
Pocillopora_meandrina_HIv1___Sc0000053 123249 423625 3.4371 9.0796
Pocillopora_meandrina_HIv1___Sc0000054 122643 2200829 17.945 18.9072
Pocillopora_meandrina_HIv1___Sc0000055 121609 846964 6.9646 14.0849
Pocillopora_meandrina_HIv1___Sc0000056 112816 128058 1.1351 10.7265
Pocillopora_meandrina_HIv1___Sc0000057 107171 459886 4.2911 9.6104
Pocillopora_meandrina_HIv1___Sc0000058 98341 97070 0.9871 9.8899
Pocillopora_meandrina_HIv1___Sc0000059 83292 1303 0.0156 0.1555
Pocillopora_meandrina_HIv1___Sc0000060 79483 795 0.01 0.1831
Pocillopora_meandrina_HIv1___Sc0000061 75390 450266 5.9725 14.0569
Pocillopora_meandrina_HIv1___Sc0000062 74194 36452 0.4913 2.2628
Pocillopora_meandrina_HIv1___Sc0000063 73457 199499 2.7159 27.381
Pocillopora_meandrina_HIv1___Sc0000064 72700 14627 0.2012 1.0648
Pocillopora_meandrina_HIv1___Sc0000065 67986 8415 0.1238 1.5823
Pocillopora_meandrina_HIv1___Sc0000066 66659 665104 9.9777 10.683
Pocillopora_meandrina_HIv1___Sc0000067 64947 268827 4.1392 8.8243
Pocillopora_meandrina_HIv1___Sc0000068 64340 10732 0.1668 1.3054
Pocillopora_meandrina_HIv1___Sc0000069 62616 285903 4.566 11.4462
Pocillopora_meandrina_HIv1___Sc0000070 60121 163335 2.7168 12.596
Pocillopora_meandrina_HIv1___Sc0000071 57157 75988 1.3295 3.0787
Pocillopora_meandrina_HIv1___Sc0000072 56626 21745 0.384 4.3438
Pocillopora_meandrina_HIv1___Sc0000073 56082 26577 0.4739 1.7649
Pocillopora_meandrina_HIv1___Sc0000074 55210 516 0.0093 0.1131
Pocillopora_meandrina_HIv1___Sc0000075 54685 1595 0.0292 0.3585
Pocillopora_meandrina_HIv1___Sc0000076 54587 331952 6.0812 31.0163
Pocillopora_meandrina_HIv1___Sc0000077 53379 35572 0.6664 1.3313
Pocillopora_meandrina_HIv1___Sc0000078 51564 0 0 0
Pocillopora_meandrina_HIv1___Sc0000079 49664 1053 0.0212 0.2016
Pocillopora_meandrina_HIv1___Sc0000080 47218 123819 2.6223 7.2653
Pocillopora_meandrina_HIv1___Sc0000081 42490 19177 0.4513 2.2327
Pocillopora_meandrina_HIv1___Sc0000082 32657 1018545 31.1892 69.6047
Pocillopora_meandrina_HIv1___Sc0000083 27992 5843 0.2087 1.1452
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 28035202 17.5044 26.8369
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3148716 2.6289 6.4434
Pocillopora_meandrina_HIv1___xfSc0000002 779520 10555840 13.5415 16.7351
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1662490 3.5958 6.9916
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1864769 5.5702 9.7611
Pocillopora_meandrina_HIv1___xfSc0000006 290100 747434 2.5765 6.3036
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1719831 6.8177 10.2604
Pocillopora_meandrina_HIv1___xfSc0000012 148278 741185 4.9986 9.2796
Pocillopora_meandrina_HIv1___xfSc0000014 118081 36019 0.305 1.171
Pocillopora_meandrina_HIv1___xfSc0000017 98555 1205607 12.2328 190.9638
Pocillopora_meandrina_HIv1___xfSc0000021 95778 692216 7.2273 15.8796
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1241348 13.6797 22.8712
Pocillopora_meandrina_HIv1___xfSc0000029 85532 410602 4.8006 11.5228
Pocillopora_meandrina_HIv1___xfSc0000038 77395 32313 0.4175 2.5828
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1819674 26.1005 29.2971
Pocillopora_meandrina_HIv1___xfSc0000059 69426 1117033 16.0895 12.4782
Pocillopora_meandrina_HIv1___xfSc0000074 66573 268705 4.0362 8.5737
Pocillopora_meandrina_HIv1___xfSc0000081 65415 545754 8.3429 9.7094
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1440583 22.0553 18.1276
Pocillopora_meandrina_HIv1___xfSc0000092 63607 1013190 15.9289 13.6107
Pocillopora_meandrina_HIv1___xfSc0000094 62842 163947 2.6089 5.7989
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1054729 17.4174 18.0103
Pocillopora_meandrina_HIv1___xfSc0000132 59032 97758 1.656 4.3027
Pocillopora_meandrina_HIv1___xfSc0000145 58221 215347 3.6988 6.882
Pocillopora_meandrina_HIv1___xfSc0000146 58151 141817 2.4388 6.1538
Pocillopora_meandrina_HIv1___xfSc0000168 56681 444571 7.8434 11.5244
Pocillopora_meandrina_HIv1___xfSc0000175 56271 372909 6.627 18.4229
Pocillopora_meandrina_HIv1___xfSc0000195 55223 8349 0.1512 1.6407
Pocillopora_meandrina_HIv1___xfSc0000199 55095 597205 10.8395 18.8936
Pocillopora_meandrina_HIv1___xfSc0000205 54658 226901 4.1513 6.7455
Pocillopora_meandrina_HIv1___xfSc0000206 54623 328992 6.023 9.5157
Pocillopora_meandrina_HIv1___xfSc0000212 54299 477328 8.7907 13.1662
Pocillopora_meandrina_HIv1___xfSc0000217 54168 547911 10.115 21.3986
Pocillopora_meandrina_HIv1___xfSc0000223 53823 568623 10.5647 12.1387
Pocillopora_meandrina_HIv1___xfSc0000228 53382 617325 11.5643 35.646
Pocillopora_meandrina_HIv1___xfSc0000237 53049 434675 8.1938 11.792
Pocillopora_meandrina_HIv1___xfSc0000262 52308 626591 11.9789 12.5177
Pocillopora_meandrina_HIv1___xfSc0000264 52264 2574490 49.2593 39.5977
Pocillopora_meandrina_HIv1___xfSc0000272 52107 645204 12.3823 16.83
Pocillopora_meandrina_HIv1___xfSc0000275 51938 710142 13.6729 15.377
Pocillopora_meandrina_HIv1___xfSc0000284 51483 465830 9.0482 13.2074
Pocillopora_meandrina_HIv1___xfSc0000288 51367 941504 18.329 21.159
Pocillopora_meandrina_HIv1___xfSc0000300 50845 9037 0.1777 0.7025
Pocillopora_meandrina_HIv1___xfSc0000301 50809 727505 14.3184 16.6216
Pocillopora_meandrina_HIv1___xfSc0000343 49544 263585 5.3202 9.598
Pocillopora_meandrina_HIv1___xfSc0000376 48519 591914 12.1996 37.8611
Pocillopora_meandrina_HIv1___xfSc0000415 47398 316320 6.6737 9.3731
Pocillopora_meandrina_HIv1___xfSc0000423 47202 76355 1.6176 4.5377
Pocillopora_meandrina_HIv1___xfSc0000426 47096 1167986 24.8001 28.2196
Pocillopora_meandrina_HIv1___xfSc0000428 47057 410591 8.7254 16.5505
Pocillopora_meandrina_HIv1___xfSc0000436 46816 388461 8.2976 12.7157
Pocillopora_meandrina_HIv1___xfSc0000445 46561 164745 3.5383 7.3825
Pocillopora_meandrina_HIv1___xfSc0000447 46542 714524 15.3522 17.9599
Pocillopora_meandrina_HIv1___xfSc0000469 45938 594438 12.94 12.4309
Pocillopora_meandrina_HIv1___xfSc0000477 45781 254213 5.5528 9.1261
Pocillopora_meandrina_HIv1___xfSc0000479 45736 219506 4.7994 7.6431
Pocillopora_meandrina_HIv1___xfSc0000482 45585 620883 13.6203 20.9475
Pocillopora_meandrina_HIv1___xfSc0000488 45379 158538 3.4936 7.1339
Pocillopora_meandrina_HIv1___xfSc0000506 44781 250422 5.5921 8.3791
Pocillopora_meandrina_HIv1___xfSc0000527 44235 336036 7.5966 10.5136
Pocillopora_meandrina_HIv1___xfSc0000540 43935 507639 11.5543 14.039
Pocillopora_meandrina_HIv1___xfSc0000555 43535 385176 8.8475 18.5494
Pocillopora_meandrina_HIv1___xfSc0000565 43357 410617 9.4706 8.9751
Pocillopora_meandrina_HIv1___xfSc0000566 43316 357416 8.2514 14.0553
Pocillopora_meandrina_HIv1___xfSc0000567 43305 299145 6.9079 12.8387
Pocillopora_meandrina_HIv1___xfSc0000570 43295 100147 2.3131 5.4746
Pocillopora_meandrina_HIv1___xfSc0000579 43029 97507 2.2661 5.5796
Pocillopora_meandrina_HIv1___xfSc0000583 42958 451473 10.5096 11.2391
Pocillopora_meandrina_HIv1___xfSc0000596 42675 251370 5.8903 10.3646
Pocillopora_meandrina_HIv1___xfSc0000612 42423 168668 3.9759 6.7965
Pocillopora_meandrina_HIv1___xfSc0000616 42355 8681868 204.9786 702.2435
Pocillopora_meandrina_HIv1___xfSc0000621 42164 653173 15.4912 15.9008
Pocillopora_meandrina_HIv1___xfSc0000642 41754 594820 14.2458 19.2243
Pocillopora_meandrina_HIv1___xfSc0000655 41446 916540 22.1141 45.8439
Pocillopora_meandrina_HIv1___xfSc0000692 40426 77557 1.9185 7.0666
Pocillopora_meandrina_HIv1___xfSc0000699 40296 34744 0.8622 2.4212
Pocillopora_meandrina_HIv1___xfSc0000704 40233 287355 7.1423 15.0158
Pocillopora_meandrina_HIv1___xfSc0000705 40197 210836 5.2451 9.7702
Pocillopora_meandrina_HIv1___xfSc0000716 39998 589314 14.7336 15.1373
Pocillopora_meandrina_HIv1___xfSc0000725 39827 144710 3.6335 12.3661
Pocillopora_meandrina_HIv1___xfSc0000729 39775 40004 1.0058 7.7703
Pocillopora_meandrina_HIv1___xfSc0000760 39228 11300 0.2881 1.7329
Pocillopora_meandrina_HIv1___xfSc0000763 39151 364906 9.3205 10.1456
Pocillopora_meandrina_HIv1___xfSc0000765 39117 107058 2.7369 8.6087
Pocillopora_meandrina_HIv1___xfSc0000788 38513 489697 12.7151 14.5266
Pocillopora_meandrina_HIv1___xfSc0000811 37888 733453 19.3585 17.7651
Pocillopora_meandrina_HIv1___xfSc0000812 37881 41256 1.0891 2.7624
Pocillopora_meandrina_HIv1___xfSc0000817 37779 599536 15.8696 13.508
Pocillopora_meandrina_HIv1___xfSc0000824 37656 171185 4.546 7.614
Pocillopora_meandrina_HIv1___xfSc0000835 37434 182564 4.877 8.5385
Pocillopora_meandrina_HIv1___xfSc0000836 37372 380687 10.1864 15.0255
Pocillopora_meandrina_HIv1___xfSc0000837 37368 474333 12.6936 15.2074
Pocillopora_meandrina_HIv1___xfSc0000840 37283 428669 11.4977 18.4951
Pocillopora_meandrina_HIv1___xfSc0000857 37006 243289 6.5743 8.3481
Pocillopora_meandrina_HIv1___xfSc0000859 36995 122953 3.3235 5.9495
Pocillopora_meandrina_HIv1___xfSc0000866 36925 87853 2.3792 4.9063
Pocillopora_meandrina_HIv1___xfSc0000868 36831 151072 4.1018 12.0443
Pocillopora_meandrina_HIv1___xfSc0000875 36611 34907 0.9535 2.9876
Pocillopora_meandrina_HIv1___xfSc0000885 36416 282202 7.7494 11.0938
Pocillopora_meandrina_HIv1___xfSc0000886 36355 86972 2.3923 7.6541
Pocillopora_meandrina_HIv1___xfSc0000890 36339 316338 8.7052 12.5958
Pocillopora_meandrina_HIv1___xfSc0000892 36267 104591 2.8839 14.2557
Pocillopora_meandrina_HIv1___xfSc0000943 35168 10774 0.3064 1.5668
Pocillopora_meandrina_HIv1___xfSc0000948 35100 345480 9.8427 13.2624
Pocillopora_meandrina_HIv1___xfSc0000952 34934 260329 7.452 9.2912
Pocillopora_meandrina_HIv1___xfSc0000953 34905 219796 6.297 8.1703
Pocillopora_meandrina_HIv1___xfSc0000957 34773 201093 5.783 11.1092
Pocillopora_meandrina_HIv1___xfSc0000968 34345 28055 0.8169 3.367
Pocillopora_meandrina_HIv1___xfSc0000974 34140 325224 9.5262 9.8728
Pocillopora_meandrina_HIv1___xfSc0000975 33988 682022 20.0666 22.6771
Pocillopora_meandrina_HIv1___xfSc0000995 33324 225976 6.7812 15.0927
Pocillopora_meandrina_HIv1___xfSc0001011 32918 333518 10.1318 18.9089
Pocillopora_meandrina_HIv1___xfSc0001122 29140 432183 14.8313 13.5586
Pocillopora_meandrina_HIv1___xfSc0001170 27381 39578 1.4455 3.8147
Pocillopora_meandrina_HIv1___xfSc0001179 27200 127026 4.6701 7.8696
Pocillopora_meandrina_HIv1___xfSc0001231 22938 21220 0.9251 1.6826
Pocillopora_meandrina_HIv1___xfSc0001237 22715 69936 3.0788 9.0115
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1203399 2.9476 7.624
Pocillopora_meandrina_HIv1___xpSc0001275 48561 277600 5.7165 11.1772
Pocillopora_meandrina_HIv1___xpSc0001276 38618 48954 1.2676 4.1271
Pocillopora_meandrina_HIv1___xpSc0001280 35955 120427 3.3494 5.5006
Pocillopora_meandrina_HIv1___xpSc0001281 34238 268957 7.8555 11.0694
Pocillopora_meandrina_HIv1___xpSc0001290 28931 271656 9.3898 10.814
Pocillopora_meandrina_HIv1___xpSc0001321 15304 126201 8.2463 14.9716
Pocillopora_meandrina_HIv1___xpSc0001331 8958 257759 28.7742 14.234
Pocillopora_meandrina_HIv1___xpSc0001337 6786 31331 4.617 10.6713
Pocillopora_meandrina_HIv1___xpSc0001344 5647 70079 12.41 16.3565
Pocillopora_meandrina_HIv1___xpSc0001355 3576 78842 22.0475 9.7158

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
    • 2025/04/23 02:06:26
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