BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6240183.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,322,394
number of mapped reads = 1,031,648 (78.01%)
number of supplementary alignments = 8,902 (0.67%)
number of secondary alignments = 0
number of mapped bases = 67,967,506 bp
number of sequenced bases = 67,935,679 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 102,375
duplication rate = 8%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.7035
>>>>>>> ACTG content
number of A's = 19,216,923 bp (28.29%)
number of C's = 12,561,829 bp (18.49%)
number of T's = 21,519,195 bp (31.68%)
number of G's = 14,592,222 bp (21.48%)
number of N's = 45,510 bp (0.07%)
GC percentage = 39.97%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 615,055
number of insertions = 4,802
mapped reads with insertion percentage = 0.46%
number of deletions = 18,277
mapped reads with deletion percentage = 1.75%
homopolymer indels = 48.29%
>>>>>>> Coverage
mean coverageData = 0.022X
std coverageData = 0.2724X
There is a 1.29% of reference with a coverageData >= 1X
There is a 0.5% of reference with a coverageData >= 2X
There is a 0.21% of reference with a coverageData >= 3X
There is a 0.09% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% 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% 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 5495616 0.022048554896077873 0.36801931373198027
chr2 243199373 7197793 0.029596264625238157 0.31816002871032967
chr3 198022430 4432667 0.022384671271835216 0.23636254085661834
chr4 191154276 4379040 0.022908407238559497 0.24027713107422616
chr5 180915260 3529282 0.019507928739676245 0.21645935867936378
chr6 171115067 3657628 0.021375253881062383 0.24903233784437928
chr7 159138663 4006882 0.02517855764566779 0.35774224730778514
chr8 146364022 3847398 0.026286500927119916 0.33038403303782526
chr9 141213431 2538638 0.017977312653780077 0.24457045891779366
chr10 135534747 3191070 0.023544294512166684 0.2707538365609265
chr11 135006516 2911803 0.021567870101914192 0.27106259320476267
chr12 133851895 3210186 0.023983119551650726 0.24183611853860612
chr13 115169878 1790512 0.01554670397410684 0.19441591836531527
chr14 107349540 2151797 0.02004477150065105 0.22901388039030712
chr15 102531392 1892041 0.01845328501928463 0.21405894406808995
chr16 90354753 2054424 0.02273730967976859 0.23929398339971505
chr17 81195210 1660517 0.0204509231517475 0.2321695197749184
chr18 78077248 1705626 0.021845365246479998 0.36188689086313125
chr19 59128983 1188298 0.020096709595022123 0.28700130526505707
chr20 63025520 1383507 0.021951536456978064 0.23438236052136605
chr21 48129895 1065890 0.022146111060495768 0.23638698030439542
chr22 51304566 647491 0.01262053361878161 0.17481165690605366
chrMT 16571 28160 1.6993542936455253 2.187364038813655
chrX 155270560 3814272 0.024565326485587482 0.2541684129826548
chrY 59373566 186968 0.003149010790424816 0.08249254663970433