Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-222-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-222-TP4_R1_001.fastp-trim.fq.gz -2 POC-222-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-222-TP4 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 20:54:27 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-222-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 49,910,316
Mapped reads 49,910,316 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 49,910,316 / 100%
Mapped reads, first in pair 24,955,158 / 50%
Mapped reads, second in pair 24,955,158 / 50%
Mapped reads, both in pair 49,910,316 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 127.67
Overlapping read pairs 18,807,798 / 75.37%
Duplicated reads (estimated) 6,728,439 / 13.48%
Duplication rate 12.8%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,532,478,732 / 39.92%
Number/percentage of C's 645,425,604 / 10.17%
Number/percentage of T's 2,533,931,645 / 39.94%
Number/percentage of G's 632,057,842 / 9.96%
Number/percentage of N's 509,722 / 0.01%
GC Percentage 20.14%

Coverage

Mean 16.8995
Standard Deviation 18.4422
Mean (paired-end reads overlap ignored) 13.03

Mapping Quality

Mean Mapping Quality 22.54

Insert size

Mean 212.39
Standard Deviation 85.62
P25/Median/P75 144 / 199 / 267

Mismatches and indels

General error rate 21.59%
Mismatches 1,346,301,067
Insertions 9,207,008
Mapped reads with at least one insertion 13.8%
Deletions 7,269,150
Mapped reads with at least one deletion 12.22%
Homopolymer indels 50.91%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 387762465 17.9096 14.1901
Pocillopora_meandrina_HIv1___Sc0000001 21507942 408931926 19.0131 13.5517
Pocillopora_meandrina_HIv1___Sc0000002 19741974 363638127 18.4195 13.65
Pocillopora_meandrina_HIv1___Sc0000003 19417450 309623797 15.9456 14.6028
Pocillopora_meandrina_HIv1___Sc0000004 14584444 248927427 17.068 29.833
Pocillopora_meandrina_HIv1___Sc0000005 14098929 253053831 17.9484 13.1332
Pocillopora_meandrina_HIv1___Sc0000006 14068054 253637620 18.0293 15.7946
Pocillopora_meandrina_HIv1___Sc0000007 13590779 249715991 18.3739 15.4133
Pocillopora_meandrina_HIv1___Sc0000008 12446599 233567996 18.7656 14.3391
Pocillopora_meandrina_HIv1___Sc0000009 11983232 118740485 9.9089 17.7627
Pocillopora_meandrina_HIv1___Sc0000010 11763137 197052271 16.7517 17.3038
Pocillopora_meandrina_HIv1___Sc0000011 10501528 218194836 20.7774 13.2708
Pocillopora_meandrina_HIv1___Sc0000012 10024633 183288789 18.2838 28.7882
Pocillopora_meandrina_HIv1___Sc0000013 9946974 139086466 13.9828 13.9553
Pocillopora_meandrina_HIv1___Sc0000014 9536826 179234207 18.7939 13.5504
Pocillopora_meandrina_HIv1___Sc0000015 9393205 160009218 17.0346 13.382
Pocillopora_meandrina_HIv1___Sc0000016 9288165 159326487 17.1537 14.4186
Pocillopora_meandrina_HIv1___Sc0000017 9274345 160570636 17.3134 13.4552
Pocillopora_meandrina_HIv1___Sc0000018 8584156 156313434 18.2095 13.4537
Pocillopora_meandrina_HIv1___Sc0000019 7112774 122841885 17.2706 15.5011
Pocillopora_meandrina_HIv1___Sc0000020 6748058 115217018 17.0741 13.681
Pocillopora_meandrina_HIv1___Sc0000021 6546105 120645157 18.4301 13.7745
Pocillopora_meandrina_HIv1___Sc0000022 6319256 102693611 16.2509 17.2262
Pocillopora_meandrina_HIv1___Sc0000023 5767069 83801861 14.5311 13.9562
Pocillopora_meandrina_HIv1___Sc0000024 5762297 67159850 11.655 17.0785
Pocillopora_meandrina_HIv1___Sc0000025 5759531 90612886 15.7327 17.207
Pocillopora_meandrina_HIv1___Sc0000026 5647578 115183518 20.3952 13.364
Pocillopora_meandrina_HIv1___Sc0000027 5550630 95413691 17.1897 21.2547
Pocillopora_meandrina_HIv1___Sc0000028 5130920 102007059 19.8809 18.1623
Pocillopora_meandrina_HIv1___Sc0000029 4860867 68922405 14.179 13.2395
Pocillopora_meandrina_HIv1___Sc0000030 4843735 91703479 18.9324 13.5784
Pocillopora_meandrina_HIv1___Sc0000031 4691590 85945552 18.3191 13.6624
Pocillopora_meandrina_HIv1___Sc0000032 3615800 72273036 19.9881 14.8807
Pocillopora_meandrina_HIv1___Sc0000033 3306609 44052902 13.3227 13.3902
Pocillopora_meandrina_HIv1___Sc0000034 3122802 60549708 19.3895 14.786
Pocillopora_meandrina_HIv1___Sc0000035 3015365 43831795 14.5361 15.4935
Pocillopora_meandrina_HIv1___Sc0000036 3007169 61877324 20.5766 13.0097
Pocillopora_meandrina_HIv1___Sc0000037 2860435 52061586 18.2006 32.552
Pocillopora_meandrina_HIv1___Sc0000038 2701138 44899225 16.6223 14.0821
Pocillopora_meandrina_HIv1___Sc0000039 2599273 34582493 13.3047 14.9344
Pocillopora_meandrina_HIv1___Sc0000040 2445666 43621750 17.8363 17.4699
Pocillopora_meandrina_HIv1___Sc0000041 2159376 41812841 19.3634 13.0999
Pocillopora_meandrina_HIv1___Sc0000042 1957488 29676688 15.1606 13.654
Pocillopora_meandrina_HIv1___Sc0000043 1845599 26203568 14.1979 12.7551
Pocillopora_meandrina_HIv1___Sc0000044 1724711 33084593 19.1827 15.7831
Pocillopora_meandrina_HIv1___Sc0000045 1153740 17940283 15.5497 14.6103
Pocillopora_meandrina_HIv1___Sc0000046 755410 9793710 12.9648 18.653
Pocillopora_meandrina_HIv1___Sc0000047 239089 1028315 4.301 6.1264
Pocillopora_meandrina_HIv1___Sc0000048 214660 83289 0.388 2.2625
Pocillopora_meandrina_HIv1___Sc0000049 179266 887644 4.9515 10.7437
Pocillopora_meandrina_HIv1___Sc0000050 177168 263284 1.4861 3.5944
Pocillopora_meandrina_HIv1___Sc0000051 165057 796711 4.8269 8.1321
Pocillopora_meandrina_HIv1___Sc0000052 155210 113349 0.7303 7.789
Pocillopora_meandrina_HIv1___Sc0000053 123249 359702 2.9185 7.401
Pocillopora_meandrina_HIv1___Sc0000054 122643 1979052 16.1367 16.5048
Pocillopora_meandrina_HIv1___Sc0000055 121609 873288 7.1811 13.9676
Pocillopora_meandrina_HIv1___Sc0000056 112816 80513 0.7137 8.8646
Pocillopora_meandrina_HIv1___Sc0000057 107171 290751 2.713 6.5165
Pocillopora_meandrina_HIv1___Sc0000058 98341 76259 0.7755 7.4678
Pocillopora_meandrina_HIv1___Sc0000059 83292 17269 0.2073 0.796
Pocillopora_meandrina_HIv1___Sc0000060 79483 1026 0.0129 0.1557
Pocillopora_meandrina_HIv1___Sc0000061 75390 391464 5.1925 11.5399
Pocillopora_meandrina_HIv1___Sc0000062 74194 18789 0.2532 0.8813
Pocillopora_meandrina_HIv1___Sc0000063 73457 76334 1.0392 11.1732
Pocillopora_meandrina_HIv1___Sc0000064 72700 10783 0.1483 0.79
Pocillopora_meandrina_HIv1___Sc0000065 67986 4370 0.0643 0.3158
Pocillopora_meandrina_HIv1___Sc0000066 66659 475700 7.1363 8.1319
Pocillopora_meandrina_HIv1___Sc0000067 64947 185405 2.8547 5.5712
Pocillopora_meandrina_HIv1___Sc0000068 64340 62783 0.9758 2.824
Pocillopora_meandrina_HIv1___Sc0000069 62616 460810 7.3593 8.9025
Pocillopora_meandrina_HIv1___Sc0000070 60121 323431 5.3797 34.1836
Pocillopora_meandrina_HIv1___Sc0000071 57157 42566 0.7447 2.0023
Pocillopora_meandrina_HIv1___Sc0000072 56626 15473 0.2732 2.5665
Pocillopora_meandrina_HIv1___Sc0000073 56082 17293 0.3084 1.166
Pocillopora_meandrina_HIv1___Sc0000074 55210 807 0.0146 0.1583
Pocillopora_meandrina_HIv1___Sc0000075 54685 6390 0.1169 0.4287
Pocillopora_meandrina_HIv1___Sc0000076 54587 189142 3.465 17.7783
Pocillopora_meandrina_HIv1___Sc0000077 53379 35476 0.6646 1.4893
Pocillopora_meandrina_HIv1___Sc0000078 51564 268 0.0052 0.0957
Pocillopora_meandrina_HIv1___Sc0000079 49664 2786 0.0561 0.3508
Pocillopora_meandrina_HIv1___Sc0000080 47218 128011 2.7111 7.3892
Pocillopora_meandrina_HIv1___Sc0000081 42490 11137 0.2621 0.9379
Pocillopora_meandrina_HIv1___Sc0000082 32657 1254938 38.4278 74.0655
Pocillopora_meandrina_HIv1___Sc0000083 27992 151572 5.4148 3.1068
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 8593497 5.3655 9.2003
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 7597613 6.3434 10.5405
Pocillopora_meandrina_HIv1___xfSc0000002 779520 11499082 14.7515 19.5872
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1472011 3.1838 5.5855
Pocillopora_meandrina_HIv1___xfSc0000004 334777 1533112 4.5795 7.8882
Pocillopora_meandrina_HIv1___xfSc0000006 290100 449380 1.5491 3.84
Pocillopora_meandrina_HIv1___xfSc0000007 252258 1728900 6.8537 10.0772
Pocillopora_meandrina_HIv1___xfSc0000012 148278 1819495 12.2708 14.4667
Pocillopora_meandrina_HIv1___xfSc0000014 118081 26911 0.2279 0.9964
Pocillopora_meandrina_HIv1___xfSc0000017 98555 669046 6.7886 103.517
Pocillopora_meandrina_HIv1___xfSc0000021 95778 612600 6.396 10.667
Pocillopora_meandrina_HIv1___xfSc0000024 90744 668149 7.363 10.6329
Pocillopora_meandrina_HIv1___xfSc0000029 85532 167251 1.9554 8.0171
Pocillopora_meandrina_HIv1___xfSc0000038 77395 72355 0.9349 10.4752
Pocillopora_meandrina_HIv1___xfSc0000058 69718 1130161 16.2105 17.353
Pocillopora_meandrina_HIv1___xfSc0000059 69426 517156 7.449 11.5642
Pocillopora_meandrina_HIv1___xfSc0000074 66573 617053 9.2688 11.5315
Pocillopora_meandrina_HIv1___xfSc0000081 65415 604436 9.24 8.4061
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1237308 18.9431 17.6052
Pocillopora_meandrina_HIv1___xfSc0000092 63607 699307 10.9942 10.928
Pocillopora_meandrina_HIv1___xfSc0000094 62842 268723 4.2762 8.7653
Pocillopora_meandrina_HIv1___xfSc0000113 60556 1078034 17.8023 16.8351
Pocillopora_meandrina_HIv1___xfSc0000132 59032 440289 7.4585 11.5346
Pocillopora_meandrina_HIv1___xfSc0000145 58221 718845 12.3468 11.1359
Pocillopora_meandrina_HIv1___xfSc0000146 58151 562307 9.6698 10.876
Pocillopora_meandrina_HIv1___xfSc0000168 56681 464740 8.1992 10.4683
Pocillopora_meandrina_HIv1___xfSc0000175 56271 213849 3.8003 7.8316
Pocillopora_meandrina_HIv1___xfSc0000195 55223 141986 2.5711 5.2844
Pocillopora_meandrina_HIv1___xfSc0000199 55095 258195 4.6864 7.8655
Pocillopora_meandrina_HIv1___xfSc0000205 54658 274611 5.0242 6.2591
Pocillopora_meandrina_HIv1___xfSc0000206 54623 287177 5.2574 8.5972
Pocillopora_meandrina_HIv1___xfSc0000212 54299 375393 6.9134 12.2588
Pocillopora_meandrina_HIv1___xfSc0000217 54168 435289 8.0359 17.0916
Pocillopora_meandrina_HIv1___xfSc0000223 53823 479965 8.9175 9.8466
Pocillopora_meandrina_HIv1___xfSc0000228 53382 350095 6.5583 34.513
Pocillopora_meandrina_HIv1___xfSc0000237 53049 420187 7.9207 8.1708
Pocillopora_meandrina_HIv1___xfSc0000262 52308 223496 4.2727 6.157
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1938769 37.0957 48.7169
Pocillopora_meandrina_HIv1___xfSc0000272 52107 649438 12.4635 17.5001
Pocillopora_meandrina_HIv1___xfSc0000275 51938 607077 11.6885 14.1064
Pocillopora_meandrina_HIv1___xfSc0000284 51483 602947 11.7116 13.8986
Pocillopora_meandrina_HIv1___xfSc0000288 51367 488732 9.5145 15.5805
Pocillopora_meandrina_HIv1___xfSc0000300 50845 12951 0.2547 0.8336
Pocillopora_meandrina_HIv1___xfSc0000301 50809 607010 11.9469 10.626
Pocillopora_meandrina_HIv1___xfSc0000343 49544 346012 6.9839 10.8606
Pocillopora_meandrina_HIv1___xfSc0000376 48519 764276 15.7521 41.3919
Pocillopora_meandrina_HIv1___xfSc0000415 47398 360163 7.5987 10.8181
Pocillopora_meandrina_HIv1___xfSc0000423 47202 88673 1.8786 5.1371
Pocillopora_meandrina_HIv1___xfSc0000426 47096 3525588 74.8596 73.7537
Pocillopora_meandrina_HIv1___xfSc0000428 47057 655261 13.9248 19.818
Pocillopora_meandrina_HIv1___xfSc0000436 46816 569632 12.1675 18.2572
Pocillopora_meandrina_HIv1___xfSc0000445 46561 260775 5.6007 6.7973
Pocillopora_meandrina_HIv1___xfSc0000447 46542 720105 15.4722 13.4008
Pocillopora_meandrina_HIv1___xfSc0000469 45938 664968 14.4753 9.6594
Pocillopora_meandrina_HIv1___xfSc0000477 45781 370705 8.0974 8.1824
Pocillopora_meandrina_HIv1___xfSc0000479 45736 172783 3.7778 5.9399
Pocillopora_meandrina_HIv1___xfSc0000482 45585 466134 10.2256 15.9595
Pocillopora_meandrina_HIv1___xfSc0000488 45379 305685 6.7363 8.9737
Pocillopora_meandrina_HIv1___xfSc0000506 44781 347891 7.7687 10.5845
Pocillopora_meandrina_HIv1___xfSc0000527 44235 342398 7.7404 9.7082
Pocillopora_meandrina_HIv1___xfSc0000540 43935 395850 9.0099 12.2817
Pocillopora_meandrina_HIv1___xfSc0000555 43535 161335 3.7059 7.7687
Pocillopora_meandrina_HIv1___xfSc0000565 43357 607901 14.0208 12.6121
Pocillopora_meandrina_HIv1___xfSc0000566 43316 475352 10.9741 17.2842
Pocillopora_meandrina_HIv1___xfSc0000567 43305 228872 5.2851 9.5583
Pocillopora_meandrina_HIv1___xfSc0000570 43295 253329 5.8512 8.9636
Pocillopora_meandrina_HIv1___xfSc0000579 43029 116067 2.6974 5.6987
Pocillopora_meandrina_HIv1___xfSc0000583 42958 333356 7.76 8.4616
Pocillopora_meandrina_HIv1___xfSc0000596 42675 888490 20.8199 11.1933
Pocillopora_meandrina_HIv1___xfSc0000612 42423 461121 10.8696 9.873
Pocillopora_meandrina_HIv1___xfSc0000616 42355 9740389 229.9702 711.631
Pocillopora_meandrina_HIv1___xfSc0000621 42164 458723 10.8795 14.1405
Pocillopora_meandrina_HIv1___xfSc0000642 41754 217991 5.2208 8.066
Pocillopora_meandrina_HIv1___xfSc0000655 41446 489931 11.8209 23.4861
Pocillopora_meandrina_HIv1___xfSc0000692 40426 291264 7.2049 8.6631
Pocillopora_meandrina_HIv1___xfSc0000699 40296 59507 1.4767 3.4442
Pocillopora_meandrina_HIv1___xfSc0000704 40233 687926 17.0986 24.2461
Pocillopora_meandrina_HIv1___xfSc0000705 40197 201050 5.0016 7.8057
Pocillopora_meandrina_HIv1___xfSc0000716 39998 267553 6.6892 9.3117
Pocillopora_meandrina_HIv1___xfSc0000725 39827 282272 7.0875 15.6994
Pocillopora_meandrina_HIv1___xfSc0000729 39775 28938 0.7275 3.6171
Pocillopora_meandrina_HIv1___xfSc0000760 39228 18614 0.4745 1.2047
Pocillopora_meandrina_HIv1___xfSc0000763 39151 406616 10.3858 7.2785
Pocillopora_meandrina_HIv1___xfSc0000765 39117 138770 3.5476 7.4727
Pocillopora_meandrina_HIv1___xfSc0000788 38513 422477 10.9697 12.6308
Pocillopora_meandrina_HIv1___xfSc0000811 37888 342925 9.051 9.5603
Pocillopora_meandrina_HIv1___xfSc0000812 37881 26357 0.6958 1.5966
Pocillopora_meandrina_HIv1___xfSc0000817 37779 612482 16.2122 8.4343
Pocillopora_meandrina_HIv1___xfSc0000824 37656 95499 2.5361 4.3275
Pocillopora_meandrina_HIv1___xfSc0000835 37434 613329 16.3843 15.9028
Pocillopora_meandrina_HIv1___xfSc0000836 37372 262990 7.0371 12.3714
Pocillopora_meandrina_HIv1___xfSc0000837 37368 228305 6.1096 8.2562
Pocillopora_meandrina_HIv1___xfSc0000840 37283 196510 5.2708 10.5376
Pocillopora_meandrina_HIv1___xfSc0000857 37006 153389 4.145 5.8047
Pocillopora_meandrina_HIv1___xfSc0000859 36995 34820 0.9412 1.9141
Pocillopora_meandrina_HIv1___xfSc0000866 36925 143993 3.8996 6.0648
Pocillopora_meandrina_HIv1___xfSc0000868 36831 146173 3.9687 8.7439
Pocillopora_meandrina_HIv1___xfSc0000875 36611 77889 2.1275 5.9388
Pocillopora_meandrina_HIv1___xfSc0000885 36416 161184 4.4262 5.4681
Pocillopora_meandrina_HIv1___xfSc0000886 36355 107128 2.9467 5.0464
Pocillopora_meandrina_HIv1___xfSc0000890 36339 274202 7.5457 10.4543
Pocillopora_meandrina_HIv1___xfSc0000892 36267 249159 6.8701 34.783
Pocillopora_meandrina_HIv1___xfSc0000943 35168 9206 0.2618 1.6561
Pocillopora_meandrina_HIv1___xfSc0000948 35100 378792 10.7918 11.3722
Pocillopora_meandrina_HIv1___xfSc0000952 34934 490558 14.0424 8.0643
Pocillopora_meandrina_HIv1___xfSc0000953 34905 247453 7.0893 10.3062
Pocillopora_meandrina_HIv1___xfSc0000957 34773 267566 7.6946 14.2972
Pocillopora_meandrina_HIv1___xfSc0000968 34345 58051 1.6902 4.2378
Pocillopora_meandrina_HIv1___xfSc0000974 34140 460792 13.4971 14.5638
Pocillopora_meandrina_HIv1___xfSc0000975 33988 279473 8.2227 9.4233
Pocillopora_meandrina_HIv1___xfSc0000995 33324 95468 2.8648 7.0351
Pocillopora_meandrina_HIv1___xfSc0001011 32918 594707 18.0663 23.022
Pocillopora_meandrina_HIv1___xfSc0001122 29140 484235 16.6175 14.7039
Pocillopora_meandrina_HIv1___xfSc0001170 27381 77805 2.8416 6.5425
Pocillopora_meandrina_HIv1___xfSc0001179 27200 121229 4.4569 6.8122
Pocillopora_meandrina_HIv1___xfSc0001231 22938 23847 1.0396 2.1132
Pocillopora_meandrina_HIv1___xfSc0001237 22715 98678 4.3442 12.4482
Pocillopora_meandrina_HIv1___xpSc0001273 408270 4083653 10.0023 13.2467
Pocillopora_meandrina_HIv1___xpSc0001275 48561 233682 4.8121 8.3968
Pocillopora_meandrina_HIv1___xpSc0001276 38618 154578 4.0027 8.0198
Pocillopora_meandrina_HIv1___xpSc0001280 35955 96029 2.6708 4.9527
Pocillopora_meandrina_HIv1___xpSc0001281 34238 299062 8.7348 12.7704
Pocillopora_meandrina_HIv1___xpSc0001290 28931 291869 10.0885 8.5824
Pocillopora_meandrina_HIv1___xpSc0001321 15304 68493 4.4755 7.5279
Pocillopora_meandrina_HIv1___xpSc0001331 8958 194368 21.6977 13.1274
Pocillopora_meandrina_HIv1___xpSc0001337 6786 26010 3.8329 7.6929
Pocillopora_meandrina_HIv1___xpSc0001344 5647 75493 13.3687 18.0601
Pocillopora_meandrina_HIv1___xpSc0001355 3576 54635 15.2782 11.199

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 20:54:29
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