BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819087.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,446,521 number of mapped reads = 1,223,104 (84.55%) number of supplementary alignments = 7,219 (0.5%) number of secondary alignments = 0 number of mapped bases = 67,685,766 bp number of sequenced bases = 67,659,297 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 187,391 duplication rate = 10.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4365 >>>>>>> ACTG content number of A's = 15,801,875 bp (23.36%) number of C's = 12,946,093 bp (19.13%) number of T's = 22,744,911 bp (33.62%) number of G's = 16,165,379 bp (23.89%) number of N's = 1,039 bp (0%) GC percentage = 43.03% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 407,601 number of insertions = 4,570 mapped reads with insertion percentage = 0.37% number of deletions = 15,654 mapped reads with deletion percentage = 1.27% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0219X std coverageData = 0.2735X There is a 1.41% of reference with a coverageData >= 1X There is a 0.44% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 6667174 0.026748876184344593 0.35330776262020935 chr2 243199373 5473504 0.022506242234432077 0.3929269720845311 chr3 198022430 3726891 0.018820549773073687 0.20301209156180108 chr4 191154276 3587393 0.018767003674037615 0.2667304067443797 chr5 180915260 3646797 0.020157486991423498 0.20874834052490088 chr6 171115067 2911447 0.01701455664333755 0.2140565914182082 chr7 159138663 3347217 0.02103333619184673 0.2670652106762807 chr8 146364022 6015801 0.0411016376688528 0.32844875635712023 chr9 141213431 2838895 0.020103576408394185 0.23262489315693205 chr10 135534747 3669425 0.027073684654459862 0.3648421529334857 chr11 135006516 2266848 0.01679065623765893 0.24188686519019786 chr12 133851895 3158531 0.02359720794389949 0.2286456497772521 chr13 115169878 1524106 0.013233547056462108 0.1684550799280441 chr14 107349540 1619534 0.015086548111896893 0.18129563648374364 chr15 102531392 1801330 0.017568570609087213 0.19511198884595665 chr16 90354753 2095938 0.023196765310176875 0.23863347488531536 chr17 81195210 2527895 0.031133548395280954 0.274681645761643 chr18 78077248 1550972 0.019864583341871887 0.3434669959048217 chr19 59128983 1477875 0.02499408792469845 0.2847284037007452 chr20 63025520 1997217 0.03168902057452283 0.2765543050405285 chr21 48129895 1004613 0.020872952247246748 0.2535848218111375 chr22 51304566 604145 0.011775657550635941 0.1571897972493197 chrMT 16571 5249 0.31675819202220745 0.8210883845343232 chrX 155270560 3820746 0.024607021446950407 0.23686957605490716 chrY 59373566 346223 0.005831265044784408 0.25052201020317166