BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472654.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 16,115,734
number of mapped reads = 15,936,240 (98.89%)
number of supplementary alignments = 107,337 (0.67%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 7,994,396
number of mapped paired reads (second in pair) = 7,941,844
number of mapped paired reads (both in pair) = 15,818,548
number of mapped paired reads (singletons) = 117,692
number of mapped bases = 1,571,982,375 bp
number of sequenced bases = 1,571,788,436 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,786,308
duplication rate = 47.73%
>>>>>>> Insert size
mean insert size = 23,257.6934
std insert size = 1,475,169.1955
median insert size = 246
>>>>>>> Mapping quality
mean mapping quality = 54.7629
>>>>>>> ACTG content
number of A's = 432,360,578 bp (27.51%)
number of C's = 355,391,371 bp (22.61%)
number of T's = 433,284,584 bp (27.57%)
number of G's = 350,455,727 bp (22.3%)
number of N's = 296,176 bp (0.02%)
GC percentage = 44.91%
>>>>>>> Mismatches and indels
general error rate = 0.0069
number of mismatches = 10,692,925
number of insertions = 110,853
mapped reads with insertion percentage = 0.69%
number of deletions = 83,839
mapped reads with deletion percentage = 0.52%
homopolymer indels = 48.51%
>>>>>>> Coverage
mean coverageData = 0.5078X
std coverageData = 21.9263X
There is a 3.44% of reference with a coverageData >= 1X
There is a 1.5% of reference with a coverageData >= 2X
There is a 0.76% of reference with a coverageData >= 3X
There is a 0.58% of reference with a coverageData >= 4X
There is a 0.46% of reference with a coverageData >= 5X
There is a 0.41% of reference with a coverageData >= 6X
There is a 0.38% of reference with a coverageData >= 7X
There is a 0.35% of reference with a coverageData >= 8X
There is a 0.34% of reference with a coverageData >= 9X
There is a 0.32% of reference with a coverageData >= 10X
There is a 0.31% of reference with a coverageData >= 11X
There is a 0.3% of reference with a coverageData >= 12X
There is a 0.29% of reference with a coverageData >= 13X
There is a 0.28% of reference with a coverageData >= 14X
There is a 0.27% of reference with a coverageData >= 15X
There is a 0.26% of reference with a coverageData >= 16X
There is a 0.25% of reference with a coverageData >= 17X
There is a 0.25% of reference with a coverageData >= 18X
There is a 0.24% of reference with a coverageData >= 19X
There is a 0.24% of reference with a coverageData >= 20X
There is a 0.23% of reference with a coverageData >= 21X
There is a 0.22% of reference with a coverageData >= 22X
There is a 0.22% of reference with a coverageData >= 23X
There is a 0.22% of reference with a coverageData >= 24X
There is a 0.21% of reference with a coverageData >= 25X
There is a 0.21% of reference with a coverageData >= 26X
There is a 0.2% of reference with a coverageData >= 27X
There is a 0.2% of reference with a coverageData >= 28X
There is a 0.2% of reference with a coverageData >= 29X
There is a 0.19% of reference with a coverageData >= 30X
There is a 0.19% of reference with a coverageData >= 31X
There is a 0.19% of reference with a coverageData >= 32X
There is a 0.18% of reference with a coverageData >= 33X
There is a 0.18% of reference with a coverageData >= 34X
There is a 0.18% of reference with a coverageData >= 35X
There is a 0.17% of reference with a coverageData >= 36X
There is a 0.17% of reference with a coverageData >= 37X
There is a 0.17% of reference with a coverageData >= 38X
There is a 0.17% of reference with a coverageData >= 39X
There is a 0.16% of reference with a coverageData >= 40X
There is a 0.16% of reference with a coverageData >= 41X
There is a 0.16% of reference with a coverageData >= 42X
There is a 0.16% of reference with a coverageData >= 43X
There is a 0.15% of reference with a coverageData >= 44X
There is a 0.15% of reference with a coverageData >= 45X
There is a 0.15% of reference with a coverageData >= 46X
There is a 0.15% of reference with a coverageData >= 47X
There is a 0.15% of reference with a coverageData >= 48X
There is a 0.14% of reference with a coverageData >= 49X
There is a 0.14% of reference with a coverageData >= 50X
There is a 0.14% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 152102114 0.6102376531290568 20.409779294576097
chr2 243199373 107127009 0.4404904818566288 18.947171427419452
chr3 198022430 154923183 0.7823516911695306 22.548093266215794
chr4 191154276 39267199 0.205421504669872 13.32145243921775
chr5 180915260 84021650 0.46442544426600607 26.05769633976638
chr6 171115067 86417746 0.505027099688422 14.176011129059384
chr7 159138663 104602715 0.6573054783047914 28.39749806712223
chr8 146364022 91118081 0.6225442547622803 20.974919039408125
chr9 141213431 74545440 0.5278919963356743 17.33822456404218
chr10 135534747 36033276 0.265860060224999 11.786601957740917
chr11 135006516 69168376 0.5123336121050631 19.072555425254695
chr12 133851895 70377410 0.5257856827503264 17.589223858776702
chr13 115169878 34059607 0.29573363792223517 14.846539158474865
chr14 107349540 67056008 0.6246510977131341 29.594712797616978
chr15 102531392 38766868 0.378097548895074 16.569531536944776
chr16 90354753 73711503 0.8158010569737266 36.34846903454044
chr17 81195210 76872343 0.9467595810146928 33.142797757834984
chr18 78077248 19274578 0.24686548890657622 11.069345702406043
chr19 59128983 53414009 0.9033473313755456 56.251764503642946
chr20 63025520 29332579 0.46540796490056724 15.186686715021942
chr21 48129895 11639063 0.24182606257503783 15.119704620179778
chr22 51304566 14803084 0.28853346113482375 11.700267338941108
chrMT 16571 13794 0.8324180797779253 1.2030147856446674
chrX 155270560 81012703 0.5217518568877448 21.964886603644068
chrY 59373566 2322037 0.03910893612150566 2.6792029387920673