BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708613.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 = 2,246,367 number of mapped reads = 1,284,290 (57.17%) number of supplementary alignments = 274 (0.01%) number of secondary alignments = 0 number of mapped bases = 61,835,535 bp number of sequenced bases = 61,818,975 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,018 duplication rate = 3.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.7505 >>>>>>> ACTG content number of A's = 17,895,600 bp (28.95%) number of C's = 11,787,634 bp (19.07%) number of T's = 19,350,523 bp (31.3%) number of G's = 12,779,979 bp (20.67%) number of N's = 5,239 bp (0.01%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 427,781 number of insertions = 3,196 mapped reads with insertion percentage = 0.25% number of deletions = 10,570 mapped reads with deletion percentage = 0.82% homopolymer indels = 48.97% >>>>>>> Coverage mean coverageData = 0.02X std coverageData = 0.2135X There is a 1.49% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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% 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 4779308 0.019174708495510628 0.25351258207802235 chr2 243199373 5247506 0.021576971746551335 0.23568824858632445 chr3 198022430 4113471 0.02077275286441036 0.18923823378686483 chr4 191154276 4313120 0.022563554895313982 0.20467878857834026 chr5 180915260 3919900 0.021667050087427673 0.19445496122469505 chr6 171115067 3579643 0.02091950792386973 0.2061019284654039 chr7 159138663 3557758 0.022356339640732057 0.268546282452265 chr8 146364022 3322577 0.022700776834350726 0.23342384807701405 chr9 141213431 2539866 0.01798600871046041 0.20273807053094292 chr10 135534747 2886943 0.021300390223918005 0.20891272381385823 chr11 135006516 2838469 0.02102468150500232 0.22532159511527497 chr12 133851895 2876734 0.02149191836245576 0.1935236007643379 chr13 115169878 1903365 0.01652658692579322 0.16958136150963707 chr14 107349540 1868315 0.017404033589710773 0.17815468968482162 chr15 102531392 1610274 0.015705180321749654 0.16390211381876524 chr16 90354753 1692237 0.018728809983023252 0.1822559789156562 chr17 81195210 1523914 0.018768520950928017 0.1982549051398448 chr18 78077248 1654611 0.02119197387694812 0.2992531280721135 chr19 59128983 1108420 0.018745798485997976 0.2789376399890777 chr20 63025520 1220936 0.01937208927431301 0.1864158469324016 chr21 48129895 812701 0.01688557600219157 0.17931920721218425 chr22 51304566 738137 0.014387354918858489 0.15601653353347314 chrMT 16571 1173 0.07078631343914067 0.29065958032055583 chrX 155270560 3550747 0.02286812773780168 0.20587181379569594 chrY 59373566 175410 0.0029543450363079087 0.08619049002845175