BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716700.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 = 1,474,686
number of mapped reads = 1,306,355 (88.59%)
number of supplementary alignments = 4,707 (0.32%)
number of secondary alignments = 0
number of mapped bases = 74,279,069 bp
number of sequenced bases = 74,256,506 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 29,343
duplication rate = 1.57%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.2895
>>>>>>> ACTG content
number of A's = 18,594,659 bp (25.04%)
number of C's = 14,960,651 bp (20.15%)
number of T's = 22,966,152 bp (30.93%)
number of G's = 17,734,445 bp (23.88%)
number of N's = 599 bp (0%)
GC percentage = 44.03%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 388,554
number of insertions = 4,846
mapped reads with insertion percentage = 0.37%
number of deletions = 14,242
mapped reads with deletion percentage = 1.08%
homopolymer indels = 41.29%
>>>>>>> Coverage
mean coverageData = 0.024X
std coverageData = 0.2122X
There is a 2.2% of reference with a coverageData >= 1X
There is a 0.15% 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 6207181 0.024903372256793694 0.2717611567182679
chr2 243199373 5831453 0.023978075798739826 0.3097720381409341
chr3 198022430 4285718 0.02164258867038446 0.1600140518976072
chr4 191154276 4514418 0.02361662053534183 0.17276575200888683
chr5 180915260 4247563 0.02347819083918073 0.16306138958156824
chr6 171115067 3966225 0.023178701148508448 0.18597000862476482
chr7 159138663 4288837 0.026950314393429334 0.2932474956554096
chr8 146364022 3856915 0.026351523737165407 0.20895378821690952
chr9 141213431 2476857 0.017539811776119227 0.16046340058051997
chr10 135534747 3357585 0.024772872450191684 0.24553852773869345
chr11 135006516 2612799 0.019353132555468656 0.18377948990799806
chr12 133851895 3678049 0.027478497782941362 0.17808470302090404
chr13 115169878 2259761 0.019621111346492873 0.15091655705638796
chr14 107349540 2506017 0.023344459603646183 0.1695949389035025
chr15 102531392 2766335 0.02698037104577689 0.1804127708122696
chr16 90354753 2582900 0.028586210622478268 0.19153387263676852
chr17 81195210 3271629 0.04029337444905925 0.22611687959727161
chr18 78077248 1392463 0.017834427258501734 0.23314130322459506
chr19 59128983 1978553 0.03346164435129892 0.25955975870258735
chr20 63025520 2351902 0.03731666156820285 0.21487452766716825
chr21 48129895 934352 0.01941313190066174 0.1571373925821486
chr22 51304566 688934 0.013428317471782142 0.12484048394450925
chrMT 16571 9229 0.5569368173314827 0.9824674536893588
chrX 155270560 3994657 0.02572707279473971 0.18094942736359196
chrY 59373566 218737 0.0036840805553097484 0.10186595762508507