BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524402.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 = 5,863,851
number of mapped reads = 5,397,196 (92.04%)
number of supplementary alignments = 21,796 (0.37%)
number of secondary alignments = 0
number of mapped bases = 317,023,578 bp
number of sequenced bases = 316,931,854 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 431,894
duplication rate = 5.81%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.7434
>>>>>>> ACTG content
number of A's = 79,547,218 bp (25.1%)
number of C's = 61,866,838 bp (19.52%)
number of T's = 103,923,549 bp (32.79%)
number of G's = 71,551,681 bp (22.58%)
number of N's = 42,568 bp (0.01%)
GC percentage = 42.1%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 1,557,525
number of insertions = 21,277
mapped reads with insertion percentage = 0.39%
number of deletions = 57,898
mapped reads with deletion percentage = 1.07%
homopolymer indels = 43.63%
>>>>>>> Coverage
mean coverageData = 0.1024X
std coverageData = 0.9216X
There is a 7.88% of reference with a coverageData >= 1X
There is a 1.58% of reference with a coverageData >= 2X
There is a 0.38% of reference with a coverageData >= 3X
There is a 0.11% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% 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 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% 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 26984281 0.10826163999808049 2.2349342106223027
chr2 243199373 25896685 0.10648335429713464 0.9831712659060485
chr3 198022430 21459003 0.1083665269636374 0.4093635214613681
chr4 191154276 21634897 0.11318029317847957 0.5226711861719812
chr5 180915260 19796470 0.10942399220496933 0.4145642703146269
chr6 171115067 12468502 0.07286618425015723 0.41589577843601355
chr7 159138663 17699712 0.11122194736548717 1.3657260025899465
chr8 146364022 16756699 0.11448646170709903 0.7496411480441773
chr9 141213431 11870901 0.0840635406698673 0.6191451469185981
chr10 135534747 15796227 0.1165474341424786 0.7457704321332231
chr11 135006516 13401407 0.09926489029610985 0.6718948642456962
chr12 133851895 14281935 0.106699535333437 0.43959174024303355
chr13 115169878 9827234 0.08532816193484202 0.363303890529396
chr14 107349540 8992286 0.08376641390359009 0.405700583318044
chr15 102531392 9721153 0.09481147978562507 0.3900683390184752
chr16 90354753 9080385 0.10049703749397666 0.45213873816675915
chr17 81195210 8372037 0.1031099864142232 0.5082638644523273
chr18 78077248 8961300 0.11477479329189472 1.2310036807234837
chr19 59128983 8730695 0.14765508481686554 1.3569220974327354
chr20 63025520 8787758 0.1394317413009841 0.506825269204668
chr21 48129895 4294223 0.08922153268774012 0.47451676477679455
chr22 51304566 2112548 0.0411766079455774 0.24980236417441773
chrMT 16571 194709 11.749984913402933 7.577367079461718
chrX 155270560 18948047 0.12203245096816807 0.5605387413707532
chrY 59373566 954484 0.01607590825856746 0.39327330945635375