BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549023.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 = 7,749,751 number of mapped reads = 6,799,633 (87.74%) number of secondary alignments = 0 number of mapped bases = 269,132,736 bp number of sequenced bases = 269,103,850 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 244,141 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0536 >>>>>>> ACTG content number of A's = 78,422,091 bp (29.14%) number of C's = 55,752,142 bp (20.72%) number of T's = 78,795,999 bp (29.28%) number of G's = 56,130,928 bp (20.86%) number of N's = 2,690 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 761,126 number of insertions = 8,816 mapped reads with insertion percentage = 0.13% number of deletions = 22,245 mapped reads with deletion percentage = 0.33% homopolymer indels = 41.24% >>>>>>> Coverage mean coverageData = 0.0869X std coverageData = 0.9012X There is a 6.91% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.07% 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% 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 21357214 0.08568570025749304 0.7467438424244318 chr2 243199373 22684713 0.09327619853690988 0.5101310567944205 chr3 198022430 18012905 0.09096396302176475 0.36305980476448874 chr4 191154276 17531712 0.0917149873225959 0.37372765483061116 chr5 180915260 16716173 0.09239780546980945 0.3711664877291765 chr6 171115067 15979906 0.09338690204293933 0.3978894841282241 chr7 159138663 14922518 0.09377053771024832 0.7383140210624184 chr8 146364022 13962816 0.09539787038648063 3.4862427236735116 chr9 141213431 11172645 0.07911885520294454 0.49633440023995645 chr10 135534747 12381550 0.09135332653847061 0.4343825335647944 chr11 135006516 12386767 0.09174940119186543 0.6047041931556677 chr12 133851895 12151260 0.09078138191469011 0.37327891736600055 chr13 115169878 8756861 0.07603429952404743 0.3309870007853384 chr14 107349540 8182190 0.07622007509300925 0.4083791857748551 chr15 102531392 7769034 0.07577224739131602 0.33135621325815456 chr16 90354753 7356575 0.0814187937628472 0.369135782891071 chr17 81195210 7040324 0.08670861249081073 0.38569275362746935 chr18 78077248 7120935 0.09120371404483929 0.877696219804987 chr19 59128983 5185436 0.0876970266848662 0.7326852092244565 chr20 63025520 5401509 0.0857035213672176 0.36143118363569776 chr21 48129895 3461032 0.07191023375388622 0.3654240233746615 chr22 51304566 2960711 0.0577085283208516 0.35651637484566623 chrMT 16571 21746 1.3122925592903265 1.8067005711412345 chrX 155270560 15825050 0.10191919189317022 0.45099311341246534 chrY 59373566 791154 0.013325020767659467 0.167192508527988