BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525176.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,865,970 number of mapped reads = 3,504,838 (90.66%) number of supplementary alignments = 11,024 (0.29%) number of secondary alignments = 0 number of mapped bases = 202,154,880 bp number of sequenced bases = 202,091,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 221,298 duplication rate = 4.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7563 >>>>>>> ACTG content number of A's = 51,068,024 bp (25.27%) number of C's = 36,737,175 bp (18.18%) number of T's = 65,933,045 bp (32.63%) number of G's = 48,348,235 bp (23.92%) number of N's = 4,641 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 1,033,046 number of insertions = 12,970 mapped reads with insertion percentage = 0.37% number of deletions = 40,212 mapped reads with deletion percentage = 1.14% homopolymer indels = 44% >>>>>>> Coverage mean coverageData = 0.0653X std coverageData = 0.563X There is a 5.4% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 21918721 0.08793848100382466 1.0841051085370428 chr2 243199373 17442258 0.07171999575837722 0.8767231153495159 chr3 198022430 16072294 0.08116400753187404 0.34537794003249306 chr4 191154276 11527422 0.06030428531978013 0.32194996480056787 chr5 180915260 9234547 0.051043494064569234 0.2686171749107511 chr6 171115067 10465999 0.06116351519179781 0.3696311820410888 chr7 159138663 11929479 0.07496279518196028 0.8238695721157103 chr8 146364022 9704925 0.06630676628987416 0.500445553199585 chr9 141213431 6748146 0.0477868567615215 0.3853375203589739 chr10 135534747 11312151 0.0834631063280031 0.5776984891435952 chr11 135006516 9475334 0.07018427169841195 0.4334066713840944 chr12 133851895 9362427 0.06994616699300372 0.32131552415832104 chr13 115169878 6343055 0.05507564226125168 0.2856754477954449 chr14 107349540 7863278 0.07324929384886046 0.33326896967019326 chr15 102531392 5633314 0.05494233414874539 0.2935380115899136 chr16 90354753 5493112 0.060794942353502975 0.34727311289369617 chr17 81195210 4133487 0.050908015386621944 0.28631827838276025 chr18 78077248 4367418 0.055937140612333056 0.8143234959863855 chr19 59128983 3779892 0.0639262136472058 0.748021612030649 chr20 63025520 3843118 0.060977172421584146 0.30158610891196413 chr21 48129895 2648123 0.05502033611334494 0.305466545259746 chr22 51304566 1679460 0.03273509808074392 0.21470228777309047 chrMT 16571 116363 7.02208677810633 5.043332304539002 chrX 155270560 10441722 0.06724856276682457 0.36098739059179696 chrY 59373566 618835 0.010422735936056122 0.26495415786606064