BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708614.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 2,156,093 number of mapped reads = 951,027 (44.11%) number of supplementary alignments = 260 (0.01%) number of secondary alignments = 0 number of mapped bases = 45,630,911 bp number of sequenced bases = 45,618,438 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,682 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4 >>>>>>> ACTG content number of A's = 13,222,813 bp (28.99%) number of C's = 8,696,769 bp (19.06%) number of T's = 14,259,830 bp (31.26%) number of G's = 9,435,192 bp (20.68%) number of N's = 3,834 bp (0.01%) GC percentage = 39.75% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 314,192 number of insertions = 2,449 mapped reads with insertion percentage = 0.26% number of deletions = 7,904 mapped reads with deletion percentage = 0.82% homopolymer indels = 47.38% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 0.1762X There is a 1.15% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.06% 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% 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 3616862 0.014510944789180686 0.20732886789927246 chr2 243199373 3860623 0.015874313129910906 0.21094483242499523 chr3 198022430 3144456 0.015879292057975454 0.16021740651270913 chr4 191154276 3223474 0.01686320634543378 0.17156253503173594 chr5 180915260 2768011 0.015300041577476659 0.18086920015598482 chr6 171115067 2705614 0.01581166432293189 0.1869695524236957 chr7 159138663 2495190 0.015679344999901125 0.18743345607326709 chr8 146364022 2376425 0.016236401319991055 0.19348043854467 chr9 141213431 1887817 0.013368537161312935 0.16531196767096737 chr10 135534747 2107670 0.015550772378687511 0.16945558578665737 chr11 135006516 2063128 0.015281692033294155 0.1790424681929384 chr12 133851895 2072426 0.015482978406842877 0.15763612501018653 chr13 115169878 1380558 0.011987144763668153 0.1392467217415022 chr14 107349540 1342710 0.01250783189196712 0.147969148775483 chr15 102531392 1330337 0.01297492381650295 0.1439796667764411 chr16 90354753 1145036 0.012672670357474167 0.14162828827923596 chr17 81195210 1092012 0.013449217016619577 0.15667032694566752 chr18 78077248 1295667 0.016594680693663794 0.23254155152299716 chr19 59128983 834418 0.014111827358843632 0.19868405464599936 chr20 63025520 973127 0.015440205808694638 0.16332485586963746 chr21 48129895 606615 0.01260370503613191 0.15234632445594132 chr22 51304566 468773 0.009137061991714344 0.11846928583016542 chrMT 16571 7243 0.43708889022991976 0.8210553438891149 chrX 155270560 2687970 0.01731152383297903 0.17093999550895428 chrY 59373566 144749 0.0024379367747593265 0.06910852204749517