BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716183.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 = 1,370,762
number of mapped reads = 1,161,535 (84.74%)
number of supplementary alignments = 4,515 (0.33%)
number of secondary alignments = 0
number of mapped bases = 66,145,500 bp
number of sequenced bases = 66,125,622 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 24,047
duplication rate = 1.44%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.4421
>>>>>>> ACTG content
number of A's = 15,854,680 bp (23.98%)
number of C's = 12,404,874 bp (18.76%)
number of T's = 21,182,700 bp (32.03%)
number of G's = 16,682,796 bp (25.23%)
number of N's = 572 bp (0%)
GC percentage = 43.99%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 348,077
number of insertions = 4,619
mapped reads with insertion percentage = 0.4%
number of deletions = 12,539
mapped reads with deletion percentage = 1.07%
homopolymer indels = 41.95%
>>>>>>> Coverage
mean coverageData = 0.0214X
std coverageData = 0.1954X
There is a 1.98% of reference with a coverageData >= 1X
There is a 0.11% of reference with a coverageData >= 2X
There is a 0.01% 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 5644961 0.022647730935843886 0.23791620632134966
chr2 243199373 5205115 0.021402666198485635 0.26790396780377956
chr3 198022430 3786824 0.019123207406352906 0.14914198669505696
chr4 191154276 4113912 0.021521422832309543 0.16924925605545565
chr5 180915260 3778908 0.02088772389902322 0.15315459491303815
chr6 171115067 3606478 0.02107633222035322 0.174456562731852
chr7 159138663 3775475 0.023724435839956756 0.27330256855272334
chr8 146364022 3426633 0.02341171657608589 0.189541853498353
chr9 141213431 2197577 0.015562096214488267 0.15153474183691373
chr10 135534747 2991715 0.022073417084697844 0.25481473206061034
chr11 135006516 2366214 0.01752666515740618 0.16623347849627493
chr12 133851895 3357743 0.025085509622407662 0.16850193330366015
chr13 115169878 2020371 0.017542529653456783 0.14019364508558024
chr14 107349540 2263783 0.021087961811480514 0.15907263500373783
chr15 102531392 2474991 0.024138860808599966 0.16822417715448892
chr16 90354753 2338058 0.025876425117337214 0.18294332990373502
chr17 81195210 2910900 0.03585063700186255 0.2100016939022249
chr18 78077248 1232204 0.01578185747530446 0.216599594396837
chr19 59128983 1646486 0.027845667496090708 0.241282929591814
chr20 63025520 1753030 0.027814605892977955 0.18271502761423378
chr21 48129895 822773 0.01709484302843378 0.14804301649948065
chr22 51304566 615093 0.011989049863515072 0.11569408156847343
chrMT 16571 4286 0.25864462011948586 0.5611743452310349
chrX 155270560 3602081 0.023198737738821834 0.1682607332366446
chrY 59373566 209889 0.0035350580088115307 0.10197144562594145