BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082682.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,365,891 number of mapped reads = 3,142,624 (93.37%) number of supplementary alignments = 15,086 (0.45%) number of secondary alignments = 0 number of mapped bases = 209,144,596 bp number of sequenced bases = 209,064,935 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,587 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8357 >>>>>>> ACTG content number of A's = 57,744,265 bp (27.62%) number of C's = 36,148,119 bp (17.29%) number of T's = 69,393,711 bp (33.19%) number of G's = 45,721,971 bp (21.87%) number of N's = 56,869 bp (0.03%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,872,936 number of insertions = 18,420 mapped reads with insertion percentage = 0.58% number of deletions = 49,371 mapped reads with deletion percentage = 1.56% homopolymer indels = 49.15% >>>>>>> Coverage mean coverageData = 0.0676X std coverageData = 0.515X There is a 5.58% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% 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 20514985 0.08230665551681815 0.894589372870345 chr2 243199373 18687462 0.07684009119546538 0.6332434571893277 chr3 198022430 18630884 0.09408471555469751 0.35909617623741474 chr4 191154276 10546002 0.05517010773015614 0.27704290544473986 chr5 180915260 11976002 0.06619674868775581 0.3002772999311728 chr6 171115067 15261837 0.08919049191617942 0.6270938760676696 chr7 159138663 10925068 0.0686512491310801 0.6522208579092424 chr8 146364022 18340440 0.1253070238804998 0.5719978690644255 chr9 141213431 5990854 0.04242410907783977 0.49570834671049346 chr10 135534747 8575047 0.06326825548285415 0.42816619337161255 chr11 135006516 8487911 0.06287038027112705 0.43824838398878646 chr12 133851895 6427171 0.048017034050956094 0.25745101688554567 chr13 115169878 5133492 0.044573217312950525 0.23989079913592123 chr14 107349540 4547654 0.04236305064744572 0.27536206470185365 chr15 102531392 4140114 0.04037898949036018 0.22920518996901937 chr16 90354753 6580823 0.07283316905309896 0.353480902251958 chr17 81195210 5255655 0.06472863362259916 0.37176153549986274 chr18 78077248 5640926 0.07224801263487156 1.0889587161598515 chr19 59128983 3359791 0.05682138994340559 0.5798010611912956 chr20 63025520 4700858 0.07458658016625647 0.33465220601399426 chr21 48129895 3614117 0.07509089724795784 0.3326084602824716 chr22 51304566 2742004 0.05344561339823048 0.2666445564120206 chrMT 16571 2954 0.1782632309456279 0.4352163238916594 chrX 155270560 8721370 0.05616885776672667 0.32915837500490874 chrY 59373566 341175 0.005746244044024575 0.11593615077261349