BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549078.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,411,267
number of mapped reads = 8,240,910 (87.56%)
number of secondary alignments = 0
number of mapped bases = 327,084,524 bp
number of sequenced bases = 327,054,226 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 307,771
duplication rate = 2.25%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.4748
>>>>>>> ACTG content
number of A's = 98,717,675 bp (30.18%)
number of C's = 64,592,396 bp (19.75%)
number of T's = 100,219,680 bp (30.64%)
number of G's = 63,441,682 bp (19.4%)
number of N's = 82,793 bp (0.03%)
GC percentage = 39.15%
>>>>>>> Mismatches and indels
general error rate = 0.0041
number of mismatches = 1,328,433
number of insertions = 8,323
mapped reads with insertion percentage = 0.1%
number of deletions = 24,486
mapped reads with deletion percentage = 0.3%
homopolymer indels = 46.09%
>>>>>>> Coverage
mean coverageData = 0.1057X
std coverageData = 0.9753X
There is a 9% of reference with a coverageData >= 1X
There is a 1.13% of reference with a coverageData >= 2X
There is a 0.17% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.01% 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 0.01% 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 26182367 0.1050443400901296 2.539144225494265
chr2 243199373 29344098 0.12065860877034416 0.7035580462485561
chr3 198022430 22939367 0.11584226594936746 0.3995691513867306
chr4 191154276 23826958 0.12464778972561409 0.4046579763245107
chr5 180915260 21453401 0.11858259496738971 0.4094056650537455
chr6 171115067 19735203 0.11533293558538595 0.5288168023543572
chr7 159138663 18841633 0.11839758261636268 1.0488323188003714
chr8 146364022 17119971 0.1169684377763273 0.6228439618062336
chr9 141213431 13941938 0.09872954648343613 0.6737368277157577
chr10 135534747 15420783 0.11377734006468466 0.9084281349037895
chr11 135006516 14970362 0.11088621826223558 0.7056748313476408
chr12 133851895 14764039 0.11030130727697206 0.42673646289633255
chr13 115169878 11862905 0.10300353882462218 0.35186260944843023
chr14 107349540 10271993 0.09568734994113622 0.47031107126325056
chr15 102531392 9337930 0.09107386350513996 0.3390906704170285
chr16 90354753 8360906 0.09253421344641383 0.5031615911331792
chr17 81195210 7061483 0.08696920668103451 0.4054427212833811
chr18 78077248 9290056 0.1189854437492469 1.571195889590594
chr19 59128983 4701952 0.07952025828010605 1.9819983250380409
chr20 63025520 6470134 0.10265895465836695 0.3912682308189129
chr21 48129895 4234155 0.08797349339739885 0.4374067028051864
chr22 51304566 2909827 0.056716725758873 0.335914470074509
chrMT 16571 12972 0.782813348621085 1.2351947793629667
chrX 155270560 11546076 0.07436101215838985 0.46751153956170227
chrY 59373566 2484015 0.04183705253614041 0.3203926581143197