Qualimap Report: BAM QC

Input data and parameters 

QualiMap command line

qualimap bamqc -bam POC-53-TP4.deduplicated.sorted.bam -nw 400 -hm 3

Alignment

Command line: "bismark -1 POC-53-TP4_R1_001.fastp-trim.fq.gz -2 POC-53-TP4_R2_001.fastp-trim.fq.gz --genome BismarkIndex --bam --score_min L,0,-0.8 --non_directional --prefix POC-53-TP4 --multicore 2"
Draw chromosome limits: no
Analyze overlapping paired-end reads: yes
Program: Bismark (v0.24.2)
Analysis date: Tue Apr 22 21:40:57 GMT 2025
Size of a homopolymer: 3
Skip duplicate alignments: no
Number of windows: 400
BAM file: POC-53-TP4.deduplicated.sorted.bam

Summary 

Globals

Reference size 376,579,914
Number of reads 47,288,102
Mapped reads 47,288,102 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 47,288,102 / 100%
Mapped reads, first in pair 23,644,051 / 50%
Mapped reads, second in pair 23,644,051 / 50%
Mapped reads, both in pair 47,288,102 / 100%
Mapped reads, singletons 0 / 0%
Secondary alignments 0
Read min/max/mean length 15 / 135 / 129.81
Overlapping read pairs 16,623,197 / 70.31%
Duplicated reads (estimated) 6,693,131 / 14.15%
Duplication rate 13.3%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 2,458,257,522 / 40.22%
Number/percentage of C's 602,836,763 / 9.86%
Number/percentage of T's 2,459,757,864 / 40.24%
Number/percentage of G's 590,706,924 / 9.66%
Number/percentage of N's 515,620 / 0.01%
GC Percentage 19.53%

Coverage

Mean 16.2814
Standard Deviation 17.3785
Mean (paired-end reads overlap ignored) 13.07

Mapping Quality

Mean Mapping Quality 22.63

Insert size

Mean 226.96
Standard Deviation 84.96
P25/Median/P75 156 / 219 / 282

Mismatches and indels

General error rate 21.2%
Mismatches 1,273,488,593
Insertions 8,861,639
Mapped reads with at least one insertion 14.18%
Deletions 7,139,365
Mapped reads with at least one deletion 12.69%
Homopolymer indels 52.17%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
Pocillopora_meandrina_HIv1___Sc0000000 21651136 376342921 17.3821 13.0647
Pocillopora_meandrina_HIv1___Sc0000001 21507942 396474554 18.4339 12.5905
Pocillopora_meandrina_HIv1___Sc0000002 19741974 356108730 18.0382 12.892
Pocillopora_meandrina_HIv1___Sc0000003 19417450 315730537 16.2601 14.4874
Pocillopora_meandrina_HIv1___Sc0000004 14584444 227118644 15.5727 20.1769
Pocillopora_meandrina_HIv1___Sc0000005 14098929 247300666 17.5404 12.721
Pocillopora_meandrina_HIv1___Sc0000006 14068054 245492387 17.4503 13.3805
Pocillopora_meandrina_HIv1___Sc0000007 13590779 230798928 16.982 14.3615
Pocillopora_meandrina_HIv1___Sc0000008 12446599 228627699 18.3687 13.6237
Pocillopora_meandrina_HIv1___Sc0000009 11983232 109046130 9.0999 15.9629
Pocillopora_meandrina_HIv1___Sc0000010 11763137 194879981 16.567 15.9895
Pocillopora_meandrina_HIv1___Sc0000011 10501528 209134996 19.9147 11.4352
Pocillopora_meandrina_HIv1___Sc0000012 10024633 170412357 16.9994 21.826
Pocillopora_meandrina_HIv1___Sc0000013 9946974 131390597 13.2091 13.1606
Pocillopora_meandrina_HIv1___Sc0000014 9536826 174516309 18.2992 12.3839
Pocillopora_meandrina_HIv1___Sc0000015 9393205 162732150 17.3245 13.3991
Pocillopora_meandrina_HIv1___Sc0000016 9288165 156082991 16.8045 13.3672
Pocillopora_meandrina_HIv1___Sc0000017 9274345 157714821 17.0055 13.2025
Pocillopora_meandrina_HIv1___Sc0000018 8584156 154925977 18.0479 12.8726
Pocillopora_meandrina_HIv1___Sc0000019 7112774 118922541 16.7196 13.957
Pocillopora_meandrina_HIv1___Sc0000020 6748058 113511647 16.8214 14.7081
Pocillopora_meandrina_HIv1___Sc0000021 6546105 119085742 18.1918 13.1758
Pocillopora_meandrina_HIv1___Sc0000022 6319256 99632492 15.7665 17.3843
Pocillopora_meandrina_HIv1___Sc0000023 5767069 86497901 14.9986 14.4887
Pocillopora_meandrina_HIv1___Sc0000024 5762297 61779631 10.7214 13.329
Pocillopora_meandrina_HIv1___Sc0000025 5759531 83875971 14.563 15.5263
Pocillopora_meandrina_HIv1___Sc0000026 5647578 110082340 19.492 11.9459
Pocillopora_meandrina_HIv1___Sc0000027 5550630 87557728 15.7744 19.9196
Pocillopora_meandrina_HIv1___Sc0000028 5130920 95099075 18.5345 14.7526
Pocillopora_meandrina_HIv1___Sc0000029 4860867 72245752 14.8627 12.9614
Pocillopora_meandrina_HIv1___Sc0000030 4843735 84617063 17.4694 11.5932
Pocillopora_meandrina_HIv1___Sc0000031 4691590 82145145 17.509 12.657
Pocillopora_meandrina_HIv1___Sc0000032 3615800 69063577 19.1005 14.0044
Pocillopora_meandrina_HIv1___Sc0000033 3306609 43120819 13.0408 14.1454
Pocillopora_meandrina_HIv1___Sc0000034 3122802 54979719 17.6059 12.6396
Pocillopora_meandrina_HIv1___Sc0000035 3015365 43237981 14.3392 14.7269
Pocillopora_meandrina_HIv1___Sc0000036 3007169 59650917 19.8362 11.6151
Pocillopora_meandrina_HIv1___Sc0000037 2860435 54236411 18.9609 19.6386
Pocillopora_meandrina_HIv1___Sc0000038 2701138 47270691 17.5003 15.7181
Pocillopora_meandrina_HIv1___Sc0000039 2599273 34899247 13.4265 14.8428
Pocillopora_meandrina_HIv1___Sc0000040 2445666 42133812 17.228 17.1763
Pocillopora_meandrina_HIv1___Sc0000041 2159376 38285875 17.7301 12.1205
Pocillopora_meandrina_HIv1___Sc0000042 1957488 26649287 13.614 12.2554
Pocillopora_meandrina_HIv1___Sc0000043 1845599 26241408 14.2184 12.2924
Pocillopora_meandrina_HIv1___Sc0000044 1724711 31211098 18.0964 13.3503
Pocillopora_meandrina_HIv1___Sc0000045 1153740 14521293 12.5863 12.1078
Pocillopora_meandrina_HIv1___Sc0000046 755410 8876330 11.7503 17.5076
Pocillopora_meandrina_HIv1___Sc0000047 239089 457358 1.9129 6.479
Pocillopora_meandrina_HIv1___Sc0000048 214660 47534 0.2214 1.208
Pocillopora_meandrina_HIv1___Sc0000049 179266 455175 2.5391 7.2895
Pocillopora_meandrina_HIv1___Sc0000050 177168 184610 1.042 3.5578
Pocillopora_meandrina_HIv1___Sc0000051 165057 790914 4.7918 7.9815
Pocillopora_meandrina_HIv1___Sc0000052 155210 108076 0.6963 8.3982
Pocillopora_meandrina_HIv1___Sc0000053 123249 290486 2.3569 6.495
Pocillopora_meandrina_HIv1___Sc0000054 122643 1545242 12.5995 13.3441
Pocillopora_meandrina_HIv1___Sc0000055 121609 634656 5.2188 11.9718
Pocillopora_meandrina_HIv1___Sc0000056 112816 70406 0.6241 6.085
Pocillopora_meandrina_HIv1___Sc0000057 107171 383262 3.5762 8.6673
Pocillopora_meandrina_HIv1___Sc0000058 98341 99530 1.0121 12.01
Pocillopora_meandrina_HIv1___Sc0000059 83292 2210 0.0265 0.1884
Pocillopora_meandrina_HIv1___Sc0000060 79483 426 0.0054 0.0927
Pocillopora_meandrina_HIv1___Sc0000061 75390 257776 3.4192 8.1984
Pocillopora_meandrina_HIv1___Sc0000062 74194 18734 0.2525 1.0614
Pocillopora_meandrina_HIv1___Sc0000063 73457 65964 0.898 10.9579
Pocillopora_meandrina_HIv1___Sc0000064 72700 8818 0.1213 0.618
Pocillopora_meandrina_HIv1___Sc0000065 67986 10554 0.1552 1.1211
Pocillopora_meandrina_HIv1___Sc0000066 66659 451871 6.7788 7.1343
Pocillopora_meandrina_HIv1___Sc0000067 64947 123436 1.9006 3.9254
Pocillopora_meandrina_HIv1___Sc0000068 64340 10687 0.1661 1.1745
Pocillopora_meandrina_HIv1___Sc0000069 62616 195399 3.1206 8.1122
Pocillopora_meandrina_HIv1___Sc0000070 60121 157039 2.612 12.6466
Pocillopora_meandrina_HIv1___Sc0000071 57157 50246 0.8791 2.2915
Pocillopora_meandrina_HIv1___Sc0000072 56626 14876 0.2627 2.8255
Pocillopora_meandrina_HIv1___Sc0000073 56082 7467 0.1331 0.575
Pocillopora_meandrina_HIv1___Sc0000074 55210 243 0.0044 0.0662
Pocillopora_meandrina_HIv1___Sc0000075 54685 284 0.0052 0.0808
Pocillopora_meandrina_HIv1___Sc0000076 54587 256532 4.6995 24.286
Pocillopora_meandrina_HIv1___Sc0000077 53379 15830 0.2966 0.8077
Pocillopora_meandrina_HIv1___Sc0000078 51564 1356 0.0263 0.338
Pocillopora_meandrina_HIv1___Sc0000079 49664 267 0.0054 0.0731
Pocillopora_meandrina_HIv1___Sc0000080 47218 111158 2.3541 7.5799
Pocillopora_meandrina_HIv1___Sc0000081 42490 10879 0.256 0.8498
Pocillopora_meandrina_HIv1___Sc0000082 32657 584945 17.9118 41.3238
Pocillopora_meandrina_HIv1___Sc0000083 27992 3934 0.1405 0.6787
Pocillopora_meandrina_HIv1___xfSc0000000 1601609 11085355 6.9214 11.332
Pocillopora_meandrina_HIv1___xfSc0000001 1197718 3799812 3.1725 7.4674
Pocillopora_meandrina_HIv1___xfSc0000002 779520 5069452 6.5033 10.0246
Pocillopora_meandrina_HIv1___xfSc0000003 462347 1505535 3.2563 5.7778
Pocillopora_meandrina_HIv1___xfSc0000004 334777 788820 2.3563 4.9376
Pocillopora_meandrina_HIv1___xfSc0000006 290100 646771 2.2295 4.6831
Pocillopora_meandrina_HIv1___xfSc0000007 252258 2729338 10.8196 16.3467
Pocillopora_meandrina_HIv1___xfSc0000012 148278 564549 3.8074 9.0241
Pocillopora_meandrina_HIv1___xfSc0000014 118081 28615 0.2423 0.9318
Pocillopora_meandrina_HIv1___xfSc0000017 98555 460049 4.6679 73.7156
Pocillopora_meandrina_HIv1___xfSc0000021 95778 630925 6.5874 13.5578
Pocillopora_meandrina_HIv1___xfSc0000024 90744 1041136 11.4733 17.2311
Pocillopora_meandrina_HIv1___xfSc0000029 85532 257483 3.0104 8.3167
Pocillopora_meandrina_HIv1___xfSc0000038 77395 18097 0.2338 1.9177
Pocillopora_meandrina_HIv1___xfSc0000058 69718 803109 11.5194 12.6353
Pocillopora_meandrina_HIv1___xfSc0000059 69426 546559 7.8725 9.497
Pocillopora_meandrina_HIv1___xfSc0000074 66573 383292 5.7575 6.7849
Pocillopora_meandrina_HIv1___xfSc0000081 65415 378505 5.7862 7.375
Pocillopora_meandrina_HIv1___xfSc0000083 65317 1030714 15.7802 14.6711
Pocillopora_meandrina_HIv1___xfSc0000092 63607 706563 11.1083 12.6038
Pocillopora_meandrina_HIv1___xfSc0000094 62842 45962 0.7314 2.1224
Pocillopora_meandrina_HIv1___xfSc0000113 60556 580544 9.5869 10.0251
Pocillopora_meandrina_HIv1___xfSc0000132 59032 44152 0.7479 1.956
Pocillopora_meandrina_HIv1___xfSc0000145 58221 316961 5.4441 6.3933
Pocillopora_meandrina_HIv1___xfSc0000146 58151 147521 2.5369 6.8586
Pocillopora_meandrina_HIv1___xfSc0000168 56681 312753 5.5178 8.3554
Pocillopora_meandrina_HIv1___xfSc0000175 56271 222140 3.9477 11.6493
Pocillopora_meandrina_HIv1___xfSc0000195 55223 8511 0.1541 1.2074
Pocillopora_meandrina_HIv1___xfSc0000199 55095 278778 5.06 10.2641
Pocillopora_meandrina_HIv1___xfSc0000205 54658 275454 5.0396 7.712
Pocillopora_meandrina_HIv1___xfSc0000206 54623 274903 5.0327 8.5109
Pocillopora_meandrina_HIv1___xfSc0000212 54299 357435 6.5827 10.8964
Pocillopora_meandrina_HIv1___xfSc0000217 54168 509492 9.4058 20.86
Pocillopora_meandrina_HIv1___xfSc0000223 53823 361093 6.7089 7.7426
Pocillopora_meandrina_HIv1___xfSc0000228 53382 369372 6.9194 30.2507
Pocillopora_meandrina_HIv1___xfSc0000237 53049 261432 4.9281 7.3908
Pocillopora_meandrina_HIv1___xfSc0000262 52308 396953 7.5888 7.6775
Pocillopora_meandrina_HIv1___xfSc0000264 52264 1120206 21.4336 25.4784
Pocillopora_meandrina_HIv1___xfSc0000272 52107 309425 5.9383 8.7964
Pocillopora_meandrina_HIv1___xfSc0000275 51938 421768 8.1206 10.6165
Pocillopora_meandrina_HIv1___xfSc0000284 51483 519140 10.0837 12.9146
Pocillopora_meandrina_HIv1___xfSc0000288 51367 337805 6.5763 13.7142
Pocillopora_meandrina_HIv1___xfSc0000300 50845 7131 0.1402 0.5792
Pocillopora_meandrina_HIv1___xfSc0000301 50809 494643 9.7353 12.0481
Pocillopora_meandrina_HIv1___xfSc0000343 49544 258034 5.2082 7.3168
Pocillopora_meandrina_HIv1___xfSc0000376 48519 569802 11.7439 39.0676
Pocillopora_meandrina_HIv1___xfSc0000415 47398 107574 2.2696 3.9967
Pocillopora_meandrina_HIv1___xfSc0000423 47202 47985 1.0166 2.8938
Pocillopora_meandrina_HIv1___xfSc0000426 47096 980111 20.8109 26.6815
Pocillopora_meandrina_HIv1___xfSc0000428 47057 701398 14.9053 25.4528
Pocillopora_meandrina_HIv1___xfSc0000436 46816 374654 8.0027 17.1179
Pocillopora_meandrina_HIv1___xfSc0000445 46561 140730 3.0225 6.5973
Pocillopora_meandrina_HIv1___xfSc0000447 46542 454021 9.7551 11.8086
Pocillopora_meandrina_HIv1___xfSc0000469 45938 480798 10.4662 9.8715
Pocillopora_meandrina_HIv1___xfSc0000477 45781 326189 7.125 8.1188
Pocillopora_meandrina_HIv1___xfSc0000479 45736 159555 3.4886 5.5307
Pocillopora_meandrina_HIv1___xfSc0000482 45585 296260 6.4991 11.7643
Pocillopora_meandrina_HIv1___xfSc0000488 45379 237001 5.2227 7.958
Pocillopora_meandrina_HIv1___xfSc0000506 44781 149150 3.3307 5.5976
Pocillopora_meandrina_HIv1___xfSc0000527 44235 267319 6.0432 8.9194
Pocillopora_meandrina_HIv1___xfSc0000540 43935 379032 8.6271 12.0467
Pocillopora_meandrina_HIv1___xfSc0000555 43535 334381 7.6807 16.6324
Pocillopora_meandrina_HIv1___xfSc0000565 43357 611902 14.1131 12.6192
Pocillopora_meandrina_HIv1___xfSc0000566 43316 236307 5.4554 9.385
Pocillopora_meandrina_HIv1___xfSc0000567 43305 174569 4.0312 8.3102
Pocillopora_meandrina_HIv1___xfSc0000570 43295 78590 1.8152 4.5122
Pocillopora_meandrina_HIv1___xfSc0000579 43029 64063 1.4888 4.0815
Pocillopora_meandrina_HIv1___xfSc0000583 42958 313978 7.309 8.1989
Pocillopora_meandrina_HIv1___xfSc0000596 42675 202132 4.7365 7.945
Pocillopora_meandrina_HIv1___xfSc0000612 42423 210055 4.9514 7.2542
Pocillopora_meandrina_HIv1___xfSc0000616 42355 9834058 232.1817 847.2503
Pocillopora_meandrina_HIv1___xfSc0000621 42164 315319 7.4784 9.32
Pocillopora_meandrina_HIv1___xfSc0000642 41754 192717 4.6155 6.8627
Pocillopora_meandrina_HIv1___xfSc0000655 41446 380658 9.1844 20.726
Pocillopora_meandrina_HIv1___xfSc0000692 40426 67265 1.6639 6.3744
Pocillopora_meandrina_HIv1___xfSc0000699 40296 34315 0.8516 2.222
Pocillopora_meandrina_HIv1___xfSc0000704 40233 717437 17.8321 24.8148
Pocillopora_meandrina_HIv1___xfSc0000705 40197 122645 3.0511 6.3888
Pocillopora_meandrina_HIv1___xfSc0000716 39998 316672 7.9172 8.5588
Pocillopora_meandrina_HIv1___xfSc0000725 39827 133376 3.3489 11.593
Pocillopora_meandrina_HIv1___xfSc0000729 39775 11225 0.2822 2.2554
Pocillopora_meandrina_HIv1___xfSc0000760 39228 5095 0.1299 0.5385
Pocillopora_meandrina_HIv1___xfSc0000763 39151 250505 6.3984 6.6157
Pocillopora_meandrina_HIv1___xfSc0000765 39117 89819 2.2962 5.2947
Pocillopora_meandrina_HIv1___xfSc0000788 38513 454064 11.7899 17.8963
Pocillopora_meandrina_HIv1___xfSc0000811 37888 287817 7.5965 9.5746
Pocillopora_meandrina_HIv1___xfSc0000812 37881 15477 0.4086 1.227
Pocillopora_meandrina_HIv1___xfSc0000817 37779 463837 12.2776 8.607
Pocillopora_meandrina_HIv1___xfSc0000824 37656 44422 1.1797 2.3626
Pocillopora_meandrina_HIv1___xfSc0000835 37434 187030 4.9963 5.9701
Pocillopora_meandrina_HIv1___xfSc0000836 37372 234563 6.2764 10.4494
Pocillopora_meandrina_HIv1___xfSc0000837 37368 106692 2.8552 6.0451
Pocillopora_meandrina_HIv1___xfSc0000840 37283 209430 5.6173 14.6872
Pocillopora_meandrina_HIv1___xfSc0000857 37006 139768 3.7769 5.6292
Pocillopora_meandrina_HIv1___xfSc0000859 36995 54302 1.4678 3.1075
Pocillopora_meandrina_HIv1___xfSc0000866 36925 50944 1.3797 3.04
Pocillopora_meandrina_HIv1___xfSc0000868 36831 92621 2.5148 8.3844
Pocillopora_meandrina_HIv1___xfSc0000875 36611 51467 1.4058 4.0193
Pocillopora_meandrina_HIv1___xfSc0000885 36416 190044 5.2187 7.4247
Pocillopora_meandrina_HIv1___xfSc0000886 36355 203736 5.6041 9.5193
Pocillopora_meandrina_HIv1___xfSc0000890 36339 224696 6.1833 11.2472
Pocillopora_meandrina_HIv1___xfSc0000892 36267 101883 2.8092 14.2703
Pocillopora_meandrina_HIv1___xfSc0000943 35168 4327 0.123 0.69
Pocillopora_meandrina_HIv1___xfSc0000948 35100 227521 6.4821 8.3615
Pocillopora_meandrina_HIv1___xfSc0000952 34934 205739 5.8894 7.7522
Pocillopora_meandrina_HIv1___xfSc0000953 34905 170186 4.8757 6.3854
Pocillopora_meandrina_HIv1___xfSc0000957 34773 259444 7.4611 8.8388
Pocillopora_meandrina_HIv1___xfSc0000968 34345 12043 0.3506 1.3363
Pocillopora_meandrina_HIv1___xfSc0000974 34140 273684 8.0165 8.9709
Pocillopora_meandrina_HIv1___xfSc0000975 33988 340669 10.0232 9.8068
Pocillopora_meandrina_HIv1___xfSc0000995 33324 84278 2.529 5.9024
Pocillopora_meandrina_HIv1___xfSc0001011 32918 129571 3.9362 8.3066
Pocillopora_meandrina_HIv1___xfSc0001122 29140 240098 8.2395 11.073
Pocillopora_meandrina_HIv1___xfSc0001170 27381 19722 0.7203 2.324
Pocillopora_meandrina_HIv1___xfSc0001179 27200 95197 3.4999 6.8179
Pocillopora_meandrina_HIv1___xfSc0001231 22938 14618 0.6373 1.3579
Pocillopora_meandrina_HIv1___xfSc0001237 22715 110195 4.8512 12.3608
Pocillopora_meandrina_HIv1___xpSc0001273 408270 1922383 4.7086 9.7879
Pocillopora_meandrina_HIv1___xpSc0001275 48561 172394 3.5501 7.2931
Pocillopora_meandrina_HIv1___xpSc0001276 38618 47998 1.2429 3.8116
Pocillopora_meandrina_HIv1___xpSc0001280 35955 162903 4.5307 7.0183
Pocillopora_meandrina_HIv1___xpSc0001281 34238 237717 6.9431 15.2799
Pocillopora_meandrina_HIv1___xpSc0001290 28931 285795 9.8785 10.587
Pocillopora_meandrina_HIv1___xpSc0001321 15304 41409 2.7058 4.9516
Pocillopora_meandrina_HIv1___xpSc0001331 8958 193603 21.6123 9.721
Pocillopora_meandrina_HIv1___xpSc0001337 6786 22998 3.389 6.5529
Pocillopora_meandrina_HIv1___xpSc0001344 5647 63468 11.2392 15.9809
Pocillopora_meandrina_HIv1___xpSc0001355 3576 40292 11.2673 9.3332

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 21:40:58
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