BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472841.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 = 2,840,474 number of mapped reads = 2,362,010 (83.16%) number of supplementary alignments = 20,041 (0.71%) number of secondary alignments = 0 number of mapped bases = 152,278,503 bp number of sequenced bases = 152,216,556 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,343 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3892 >>>>>>> ACTG content number of A's = 41,333,122 bp (27.15%) number of C's = 29,811,815 bp (19.59%) number of T's = 45,577,787 bp (29.94%) number of G's = 35,489,972 bp (23.32%) number of N's = 3,860 bp (0%) GC percentage = 42.9% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,248,388 number of insertions = 11,993 mapped reads with insertion percentage = 0.5% number of deletions = 34,549 mapped reads with deletion percentage = 1.45% homopolymer indels = 46.17% >>>>>>> Coverage mean coverageData = 0.0492X std coverageData = 0.34X There is a 4.24% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11040780 0.044295897661976134 0.4145492662384823 chr2 243199373 14727229 0.06055619641749652 0.492519305980349 chr3 198022430 11304373 0.05708632602882411 0.267848311569931 chr4 191154276 8503260 0.04448375510051368 0.2628382713370577 chr5 180915260 6853022 0.037879734412674754 0.21995027372183026 chr6 171115067 9638835 0.05632955162271012 0.28862555475416846 chr7 159138663 9377721 0.05892798659493576 0.44097200598934444 chr8 146364022 8668950 0.05922869487694182 0.3569225544847117 chr9 141213431 9060921 0.06416472523778563 0.4100900566301298 chr10 135534747 6400562 0.04722450988896596 0.3028733190080457 chr11 135006516 5203226 0.03854055459071323 0.3318292605003241 chr12 133851895 6494302 0.04851856598668252 0.25436450990200105 chr13 115169878 6271653 0.0544556711260908 0.27023161875174223 chr14 107349540 3173173 0.02955926033777136 0.22885080197067173 chr15 102531392 2927282 0.028550104927864434 0.2055305668958258 chr16 90354753 4162088 0.04606385233547149 0.2701020819883525 chr17 81195210 3426782 0.042204238402733366 0.250975400767233 chr18 78077248 2640150 0.03381458834204812 0.6005326599324623 chr19 59128983 3628166 0.061360196234053276 0.37298188301775737 chr20 63025520 6629152 0.10518202785157504 0.3927912340823241 chr21 48129895 2310817 0.048012093107620536 0.287876838119554 chr22 51304566 1392019 0.02713245834688476 0.1914568825680919 chrMT 16571 27522 1.660853297930119 1.8140973188309266 chrX 155270560 7650825 0.049274150875735875 0.27752397311330546 chrY 59373566 765693 0.012896193568700252 0.1688470283674966