BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716509.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 = 1,502,044
number of mapped reads = 1,336,649 (88.99%)
number of supplementary alignments = 5,947 (0.4%)
number of secondary alignments = 0
number of mapped bases = 76,774,818 bp
number of sequenced bases = 76,754,279 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 49,938
duplication rate = 2.77%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.1391
>>>>>>> ACTG content
number of A's = 19,615,699 bp (25.56%)
number of C's = 13,500,370 bp (17.59%)
number of T's = 24,339,967 bp (31.71%)
number of G's = 19,296,109 bp (25.14%)
number of N's = 2,134 bp (0%)
GC percentage = 42.73%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 379,048
number of insertions = 5,224
mapped reads with insertion percentage = 0.39%
number of deletions = 13,114
mapped reads with deletion percentage = 0.97%
homopolymer indels = 42.29%
>>>>>>> Coverage
mean coverageData = 0.0248X
std coverageData = 0.2529X
There is a 2.23% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 8531383 0.03422813137143598 0.4636786611152457
chr2 243199373 6565706 0.026997215983776406 0.3193464562866525
chr3 198022430 6882753 0.034757441366616904 0.20581647050147167
chr4 191154276 3638022 0.01903186303820899 0.15997618662094887
chr5 180915260 3422621 0.018918365426996042 0.15375327608113426
chr6 171115067 5426681 0.03171363629831615 0.2516400837005249
chr7 159138663 4532375 0.028480665317641887 0.3254773693335551
chr8 146364022 5079858 0.034707012902392094 0.22939312165836775
chr9 141213431 2851225 0.020190891049166562 0.20478920149583998
chr10 135534747 3994252 0.029470317305421316 0.29852516804792556
chr11 135006516 2550091 0.018888651270728297 0.19599745314353292
chr12 133851895 3402065 0.02541663679845549 0.17754665063621963
chr13 115169878 1744784 0.015149655711192122 0.13545135577424194
chr14 107349540 1790596 0.016680052844194767 0.1529147953323879
chr15 102531392 2248145 0.021926406695034435 0.16395113289403407
chr16 90354753 1638238 0.01813117678491136 0.164884650333197
chr17 81195210 1672942 0.020603949420168997 0.16208027473372363
chr18 78077248 1499296 0.01920272599771959 0.34008656637705015
chr19 59128983 1625026 0.027482732114638263 0.31489972552049
chr20 63025520 1177807 0.018687779172627216 0.15076295156370959
chr21 48129895 706801 0.01468528032317544 0.14497739167793108
chr22 51304566 1203433 0.02345664516487675 0.16830667699667842
chrMT 16571 127197 7.675879548609016 5.097668837651962
chrX 155270560 4261182 0.02744359265529795 0.20372520415138096
chrY 59373566 202339 0.0034078970429365823 0.08437281550075844