BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006446.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,927,913 number of mapped reads = 1,848,613 (95.89%) number of supplementary alignments = 6,081 (0.32%) number of secondary alignments = 0 number of mapped bases = 105,023,909 bp number of sequenced bases = 104,993,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,191 duplication rate = 1.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2348 >>>>>>> ACTG content number of A's = 30,253,219 bp (28.81%) number of C's = 21,726,788 bp (20.69%) number of T's = 30,290,532 bp (28.85%) number of G's = 22,720,440 bp (21.64%) number of N's = 2,944 bp (0%) GC percentage = 42.33% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 427,655 number of insertions = 6,399 mapped reads with insertion percentage = 0.35% number of deletions = 18,336 mapped reads with deletion percentage = 0.99% homopolymer indels = 47.06% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.2866X There is a 3.01% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 8409180 0.03373784974441448 0.39240733480137036 chr2 243199373 9018133 0.03708123458032106 0.2453475358907073 chr3 198022430 7136165 0.03603715498289765 0.20716872307795625 chr4 191154276 6901176 0.036102650405790554 0.2105882341907118 chr5 180915260 6309594 0.03487596347593896 0.20457420976402693 chr6 171115067 6085261 0.03556239147543916 0.2173689354071215 chr7 159138663 5740127 0.03606997125519397 0.26932386267833147 chr8 146364022 5516995 0.03769365534379754 0.7282383091321789 chr9 141213431 4431756 0.03138338873729369 0.22596944800897215 chr10 135534747 5090477 0.03755846462014645 0.2634421062305549 chr11 135006516 4820568 0.035706187692451825 0.23667527066734348 chr12 133851895 4818457 0.035998421987227004 0.21022160919485497 chr13 115169878 3427846 0.029763390041969134 0.18952661722453673 chr14 107349540 3222112 0.030015144918180366 0.19847000500445422 chr15 102531392 3148961 0.03071216471926959 0.19161310078813668 chr16 90354753 3166249 0.03504241774641341 0.22137062984582204 chr17 81195210 3032114 0.03734350831779362 0.23244287918116546 chr18 78077248 2891917 0.03703917689312 0.3385831504680023 chr19 59128983 2170151 0.03670198420290773 0.31643744503319693 chr20 63025520 2317982 0.03677846688135219 0.21235111866070552 chr21 48129895 1993079 0.04141041654048903 0.23864549819236622 chr22 51304566 1369570 0.026694894953404342 0.19314490264432546 chrMT 16571 66796 4.030897350793555 2.724897759434833 chrX 155270560 3152124 0.020300847758905487 0.1642709470441832 chrY 59373566 787119 0.013257061231592523 0.1576393683782814