BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524728.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 = 1,349,659
number of mapped reads = 1,232,420 (91.31%)
number of supplementary alignments = 4,381 (0.32%)
number of secondary alignments = 0
number of mapped bases = 70,272,532 bp
number of sequenced bases = 70,249,643 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 49,339
duplication rate = 3.09%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.6675
>>>>>>> ACTG content
number of A's = 16,307,253 bp (23.21%)
number of C's = 12,842,367 bp (18.28%)
number of T's = 22,903,342 bp (32.6%)
number of G's = 18,188,643 bp (25.89%)
number of N's = 8,038 bp (0.01%)
GC percentage = 44.17%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 357,075
number of insertions = 4,800
mapped reads with insertion percentage = 0.39%
number of deletions = 14,118
mapped reads with deletion percentage = 1.13%
homopolymer indels = 43.04%
>>>>>>> Coverage
mean coverageData = 0.0227X
std coverageData = 0.2159X
There is a 2.03% of reference with a coverageData >= 1X
There is a 0.17% 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 5563575 0.02232120817865485 0.28959488015305135
chr2 243199373 5957505 0.024496383056053356 0.33155854937167906
chr3 198022430 4641371 0.02343861248445441 0.16981601086254194
chr4 191154276 4500017 0.023541283481411632 0.18821795466160007
chr5 180915260 4233382 0.02339980607495465 0.16738341797737033
chr6 171115067 3951938 0.023095207624235684 0.18249438492795791
chr7 159138663 3859997 0.024255557557373724 0.2554600904609632
chr8 146364022 3472759 0.023726862329596272 0.20014228645564638
chr9 141213431 3047724 0.021582394666127755 0.19165779497074906
chr10 135534747 3428050 0.025292776028865867 0.257228497697881
chr11 135006516 3130096 0.0231847772443813 0.19059671109464155
chr12 133851895 3165977 0.023652836592264907 0.1708875506221094
chr13 115169878 2164736 0.018796025815013887 0.1525745481141862
chr14 107349540 2123464 0.01978083930308411 0.15696660638409723
chr15 102531392 2041810 0.01991399863175563 0.1553856185183063
chr16 90354753 2114916 0.023406804067075477 0.18243264667426187
chr17 81195210 1974179 0.024313983546566355 0.17746050060560795
chr18 78077248 1846386 0.023648195182289212 0.2886586907520876
chr19 59128983 1523642 0.025768107663884564 0.24892261024289003
chr20 63025520 1503226 0.023851068583012086 0.1763401968315472
chr21 48129895 919626 0.01910716821634454 0.16477041103681245
chr22 51304566 876362 0.017081559563333994 0.14405489028018093
chrMT 16571 27474 1.657956671293223 1.628390069729545
chrX 155270560 3959561 0.025501041536785854 0.18601551468939692
chrY 59373566 244759 0.004122356403521392 0.12245907118996638