BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548967.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 7,177,201 number of mapped reads = 6,289,585 (87.63%) number of secondary alignments = 0 number of mapped bases = 248,821,640 bp number of sequenced bases = 248,798,152 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 279,304 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.0008 >>>>>>> ACTG content number of A's = 70,555,067 bp (28.36%) number of C's = 52,916,098 bp (21.27%) number of T's = 72,027,797 bp (28.95%) number of G's = 53,298,836 bp (21.42%) number of N's = 354 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 734,616 number of insertions = 7,961 mapped reads with insertion percentage = 0.13% number of deletions = 18,074 mapped reads with deletion percentage = 0.29% homopolymer indels = 39.69% >>>>>>> Coverage mean coverageData = 0.0804X std coverageData = 0.7327X There is a 6.65% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% 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 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 20308702 0.08147904273426063 1.1955880999340793 chr2 243199373 20924166 0.08603708859068482 0.7670730031949563 chr3 198022430 16388721 0.08276194267487778 0.33708934784012257 chr4 191154276 16722060 0.08747939282299916 0.3976018874716881 chr5 180915260 15740561 0.08700515921100299 0.36208007780573637 chr6 171115067 14836717 0.08670608182036944 0.37785279402491095 chr7 159138663 14289296 0.0897914795224841 1.201333305854942 chr8 146364022 12980135 0.08868391851106688 1.243552968787811 chr9 141213431 10556437 0.07475519095630499 0.7984838796838303 chr10 135534747 12013570 0.08863830320943455 0.5958119287616509 chr11 135006516 11666358 0.08641329578492345 0.5703626196050188 chr12 133851895 11095842 0.0828964132334473 0.37253475272732445 chr13 115169878 7867682 0.06831371307000951 0.2987382496672734 chr14 107349540 7708590 0.07180831888054667 0.46310322039389035 chr15 102531392 7124456 0.06948560690563921 0.31064406780954856 chr16 90354753 7115460 0.07875025677951884 0.4228419990152845 chr17 81195210 6714025 0.08268991483610917 0.36877422857115694 chr18 78077248 6876734 0.08807602952399142 1.5393107467525222 chr19 59128983 5343471 0.09036974304124257 1.1876700406513168 chr20 63025520 5158886 0.08185392203031407 0.3696564824714729 chr21 48129895 3229036 0.06709002793378212 0.4559319556245735 chr22 51304566 2847250 0.055497009759326296 0.3613535459831695 chrMT 16571 6600 0.39828616257317 0.7520138242922692 chrX 155270560 9032619 0.058173416776496456 0.4557105756334733 chrY 59373566 2274266 0.038304352479013974 0.3742441878359002