BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6237856.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 = 3,227,569
number of mapped reads = 2,696,636 (83.55%)
number of supplementary alignments = 23,710 (0.73%)
number of secondary alignments = 0
number of mapped bases = 196,874,507 bp
number of sequenced bases = 196,788,744 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 205,456
duplication rate = 6%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.9508
>>>>>>> ACTG content
number of A's = 58,345,558 bp (29.65%)
number of C's = 39,454,868 bp (20.05%)
number of T's = 58,883,961 bp (29.92%)
number of G's = 39,748,371 bp (20.2%)
number of N's = 355,986 bp (0.18%)
GC percentage = 40.25%
>>>>>>> Mismatches and indels
general error rate = 0.0088
number of mismatches = 1,690,129
number of insertions = 16,103
mapped reads with insertion percentage = 0.59%
number of deletions = 46,513
mapped reads with deletion percentage = 1.7%
homopolymer indels = 48.01%
>>>>>>> Coverage
mean coverageData = 0.0636X
std coverageData = 0.7889X
There is a 2.09% of reference with a coverageData >= 1X
There is a 1.2% of reference with a coverageData >= 2X
There is a 0.82% of reference with a coverageData >= 3X
There is a 0.59% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.31% of reference with a coverageData >= 6X
There is a 0.23% of reference with a coverageData >= 7X
There is a 0.16% of reference with a coverageData >= 8X
There is a 0.12% of reference with a coverageData >= 9X
There is a 0.08% of reference with a coverageData >= 10X
There is a 0.06% of reference with a coverageData >= 11X
There is a 0.04% of reference with a coverageData >= 12X
There is a 0.03% of reference with a coverageData >= 13X
There is a 0.02% of reference with a coverageData >= 14X
There is a 0.02% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% 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 8003820 0.032111534839465855 1.2183460388028322
chr2 243199373 21533092 0.08854090261161982 1.0000041455528046
chr3 198022430 29919056 0.15108922761931565 0.959189358099269
chr4 191154276 6505607 0.03403328000886572 0.4765639236393657
chr5 180915260 5276479 0.029165472276910194 0.4049513654506251
chr6 171115067 5918759 0.034589350334649376 0.44769931231124055
chr7 159138663 4042076 0.02539971069129819 0.510325835388482
chr8 146364022 7673272 0.05242594385661252 0.8538639970729952
chr9 141213431 10159768 0.07194618761157358 0.832495522014011
chr10 135534747 15519503 0.1145057141693709 1.0202701495812465
chr11 135006516 3830189 0.028370401025680864 0.42325780978955524
chr12 133851895 9326102 0.06967478495541658 0.6487001011756391
chr13 115169878 5502024 0.04777311650881492 0.5276238675823692
chr14 107349540 4858106 0.04525502391533303 0.5157693746474732
chr15 102531392 12736248 0.12421803460934189 0.849009023117202
chr16 90354753 4400985 0.04870784163396474 0.5570945141197374
chr17 81195210 12024659 0.1480956696829776 0.915360492318365
chr18 78077248 6421226 0.0822419611920748 1.4580494297604158
chr19 59128983 4388718 0.07422278850965525 0.8111262635203585
chr20 63025520 4775663 0.07577348032987273 0.669724811879364
chr21 48129895 2172555 0.04513940867728882 0.5334975728399374
chr22 51304566 3853567 0.07511157973736685 0.6267507074508365
chrMT 16571 109965 6.63599058596343 6.125909160620078
chrX 155270560 7386184 0.047569764673998725 0.5462369018760106
chrY 59373566 536884 0.009042475232159713 0.3344980023784367