BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716197.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 = 5,227,830
number of mapped reads = 2,695,334 (51.56%)
number of supplementary alignments = 70,114 (1.34%)
number of secondary alignments = 0
number of mapped bases = 200,993,657 bp
number of sequenced bases = 200,923,394 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 109,031
duplication rate = 2.91%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.9321
>>>>>>> ACTG content
number of A's = 53,490,314 bp (26.62%)
number of C's = 39,958,846 bp (19.89%)
number of T's = 59,785,168 bp (29.76%)
number of G's = 47,665,032 bp (23.72%)
number of N's = 24,034 bp (0.01%)
GC percentage = 43.61%
>>>>>>> Mismatches and indels
general error rate = 0.0075
number of mismatches = 1,480,193
number of insertions = 16,417
mapped reads with insertion percentage = 0.6%
number of deletions = 40,655
mapped reads with deletion percentage = 1.49%
homopolymer indels = 40.21%
>>>>>>> Coverage
mean coverageData = 0.0649X
std coverageData = 0.4599X
There is a 5.27% of reference with a coverageData >= 1X
There is a 0.85% of reference with a coverageData >= 2X
There is a 0.19% of reference with a coverageData >= 3X
There is a 0.05% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 16042815 0.06436419269743765 0.5360926690652541
chr2 243199373 17116773 0.07038164938032139 0.7192896887503192
chr3 198022430 13421442 0.06777738259246692 0.30799130516571066
chr4 191154276 12665736 0.06625923450438535 0.3389471988613618
chr5 180915260 12285004 0.06790474170061718 0.3131510204550592
chr6 171115067 11681533 0.06826712109460238 0.3487740947737482
chr7 159138663 11071656 0.06957238292243287 0.5337129543882715
chr8 146364022 10264827 0.07013217360206185 0.5929475818968892
chr9 141213431 8574250 0.06071837458577152 0.48995180240035263
chr10 135534747 9489797 0.07001744726022177 0.4536443979616584
chr11 135006516 9143967 0.0677298197962534 0.4999896283017048
chr12 133851895 9112412 0.06807831895095695 0.3166291300691443
chr13 115169878 6357350 0.05519976325754205 0.278285133376675
chr14 107349540 6054167 0.05639676704716201 0.3520652113665107
chr15 102531392 5634523 0.0549541256593883 0.28330028815853625
chr16 90354753 5941070 0.06575271142626 0.34632235409363954
chr17 81195210 5525031 0.06804626775397218 0.3433477062561361
chr18 78077248 5526019 0.07077630348856558 0.8965233112292466
chr19 59128983 4109259 0.06949652761658356 0.4988035558704817
chr20 63025520 4296064 0.06816388028214602 0.3303413227105982
chr21 48129895 2634940 0.05474643150582398 0.31505877961298584
chr22 51304566 2283516 0.0445090208929942 0.25512570491646364
chrMT 16571 27461 1.6571721682457305 1.7862012715785078
chrX 155270560 11233036 0.07234491844429491 0.4069080554926777
chrY 59373566 501009 0.008438250112853252 0.22213835772448573