BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237612.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 = 1,251,360 number of mapped reads = 937,256 (74.9%) number of supplementary alignments = 2,903 (0.23%) number of secondary alignments = 0 number of mapped bases = 54,859,252 bp number of sequenced bases = 54,822,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,488 duplication rate = 7.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5623 >>>>>>> ACTG content number of A's = 13,629,825 bp (24.86%) number of C's = 9,015,572 bp (16.44%) number of T's = 18,264,413 bp (33.32%) number of G's = 13,820,067 bp (25.21%) number of N's = 92,751 bp (0.17%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 542,984 number of insertions = 4,924 mapped reads with insertion percentage = 0.52% number of deletions = 22,828 mapped reads with deletion percentage = 2.4% homopolymer indels = 48.84% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 0.2155X There is a 1.36% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.03% 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% 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 4467376 0.017923229166197343 0.2420661656051744 chr2 243199373 4688708 0.019279276678069397 0.33798994781138797 chr3 198022430 3963983 0.020017848483123855 0.18858388192473907 chr4 191154276 3425854 0.01792193233490628 0.17528640180119368 chr5 180915260 2982221 0.016484076578172566 0.16513610391502787 chr6 171115067 3259281 0.019047305752450193 0.21294118352897112 chr7 159138663 3117915 0.019592441844255033 0.2693662776416545 chr8 146364022 2797528 0.01911349498171074 0.20394789664977211 chr9 141213431 2185296 0.015475128566205575 0.19088825729427356 chr10 135534747 2640984 0.01948566001307399 0.2009223610624775 chr11 135006516 2300270 0.017038214659209485 0.18681233250795323 chr12 133851895 2794154 0.02087496781423976 0.19518670207158886 chr13 115169878 1886757 0.016382382553188083 0.17792246985349683 chr14 107349540 1654846 0.015415492232197734 0.1658485048438123 chr15 102531392 1734385 0.01691564862398435 0.1719584618492622 chr16 90354753 1466416 0.016229539136695996 0.17101726816062954 chr17 81195210 1486197 0.018303998474786875 0.17531919334414384 chr18 78077248 1469844 0.018825509833543315 0.36085464209345924 chr19 59128983 1032588 0.017463314056999763 0.2076136979116758 chr20 63025520 1134582 0.01800194587843147 0.1897681665819586 chr21 48129895 729619 0.015159372360982712 0.16331948138159444 chr22 51304566 614812 0.011983572768162584 0.14042308334518186 chrMT 16571 27570 1.6637499245670146 2.1215486168970585 chrX 155270560 2823755 0.018186029598914306 0.18257992422613611 chrY 59373566 174311 0.0029358351155798863 0.07538592908561684