BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819015.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 = 2,628,667 number of mapped reads = 1,442,524 (54.88%) number of supplementary alignments = 19,590 (0.75%) number of secondary alignments = 0 number of mapped bases = 133,506,394 bp number of sequenced bases = 133,426,863 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 453,867 duplication rate = 25.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1176 >>>>>>> ACTG content number of A's = 38,832,495 bp (29.1%) number of C's = 29,021,584 bp (21.75%) number of T's = 37,429,349 bp (28.05%) number of G's = 28,136,631 bp (21.09%) number of N's = 6,804 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 845,928 number of insertions = 21,341 mapped reads with insertion percentage = 1.43% number of deletions = 42,406 mapped reads with deletion percentage = 2.88% homopolymer indels = 42.06% >>>>>>> Coverage mean coverageData = 0.0431X std coverageData = 0.535X There is a 2.61% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 13373629 0.053655348766412904 0.9138591350156519 chr2 243199373 10765248 0.044265114120997345 0.7870947960042386 chr3 198022430 7215538 0.03643798331330446 0.29038614838225346 chr4 191154276 7344929 0.03842408945118235 0.3490005035851216 chr5 180915260 7169052 0.03962657434204279 0.3207158115900321 chr6 171115067 5582213 0.03262256853161855 0.3492132396457773 chr7 159138663 6669870 0.04191231643060869 0.6715354983518964 chr8 146364022 12104042 0.0826982057106903 0.4992817016053803 chr9 141213431 5772898 0.04088065815779237 0.5171244702209575 chr10 135534747 6966080 0.0513970044891883 0.6634662251990929 chr11 135006516 4553952 0.033731349677966656 0.335079772537391 chr12 133851895 6114001 0.04567735854617523 0.3345869566010798 chr13 115169878 2935128 0.02548520542845413 0.24358896184275328 chr14 107349540 3143229 0.029280321089405693 0.27985085634663687 chr15 102531392 3563240 0.03475267360068612 0.2907493457609527 chr16 90354753 4321040 0.04782305143371927 0.6229647540646249 chr17 81195210 4641051 0.0571591723206332 0.43161386316399875 chr18 78077248 3213886 0.04116290061862836 0.6127892068324943 chr19 59128983 2779751 0.04701164909262857 0.826653695942077 chr20 63025520 3820011 0.06061054315775578 0.412954915431404 chr21 48129895 1865280 0.038755122985412706 0.34535696948586275 chr22 51304566 1083402 0.021117067825892923 0.2542131587800092 chrMT 16571 38164 2.303059561885221 2.5430996225622047 chrX 155270560 7967247 0.051312025924296276 0.4339344013879044 chrY 59373566 503513 0.008480423762992441 0.5563146475298943