BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524941.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 604,299
number of mapped reads = 557,186 (92.2%)
number of supplementary alignments = 2,340 (0.39%)
number of secondary alignments = 0
number of mapped bases = 32,657,864 bp
number of sequenced bases = 32,647,266 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 12,305
duplication rate = 1.71%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.101
>>>>>>> ACTG content
number of A's = 8,470,417 bp (25.95%)
number of C's = 5,866,481 bp (17.97%)
number of T's = 10,192,658 bp (31.22%)
number of G's = 8,117,448 bp (24.86%)
number of N's = 262 bp (0%)
GC percentage = 42.83%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 160,899
number of insertions = 2,282
mapped reads with insertion percentage = 0.41%
number of deletions = 6,334
mapped reads with deletion percentage = 1.13%
homopolymer indels = 42.54%
>>>>>>> Coverage
mean coverageData = 0.0105X
std coverageData = 0.1275X
There is a 0.99% of reference with a coverageData >= 1X
There is a 0.04% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 3101352 0.012442705207944096 0.19560984306811022
chr2 243199373 2828336 0.01162970103545456 0.1430510880807977
chr3 198022430 2356855 0.011901959793140605 0.11354175085838458
chr4 191154276 1489948 0.007794479052092981 0.10020329855632246
chr5 180915260 2024412 0.011189835506413334 0.11011103193819716
chr6 171115067 2110357 0.012332970070952314 0.11821304637175102
chr7 159138663 1988951 0.0124982261538794 0.14437022242904263
chr8 146364022 2899369 0.019809301222946715 0.17146776647963477
chr9 141213431 1175619 0.008325121708855016 0.10775091557032695
chr10 135534747 1456569 0.010746830847738255 0.13522521686432515
chr11 135006516 1668660 0.012359847875786973 0.12628848913515148
chr12 133851895 1102113 0.00823382440719274 0.0955722827924174
chr13 115169878 812583 0.007055516721134323 0.08764296150896865
chr14 107349540 611635 0.005697602430341108 0.0792823432349824
chr15 102531392 836541 0.008158876844274191 0.09425406773967324
chr16 90354753 943669 0.010444043823571739 0.10896955981898937
chr17 81195210 745589 0.009182672229063759 0.10135483306074607
chr18 78077248 872249 0.011171615577434287 0.1640266532346591
chr19 59128983 658385 0.011134725587957433 0.16005806283282561
chr20 63025520 569546 0.009036752096611023 0.09995311107421326
chr21 48129895 288566 0.005995566788583271 0.08758059294794691
chr22 51304566 555560 0.01082866581504656 0.10800137776880143
chrMT 16571 1830 0.11043389053165167 0.32009763125100005
chrX 155270560 1468422 0.009457182353177575 0.10521667103554512
chrY 59373566 90748 0.0015284242822807713 0.06805916880100724