BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549080.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,703,605 number of mapped reads = 7,577,654 (87.06%) number of secondary alignments = 0 number of mapped bases = 301,054,851 bp number of sequenced bases = 301,027,666 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 288,050 duplication rate = 2.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1578 >>>>>>> ACTG content number of A's = 90,217,282 bp (29.97%) number of C's = 60,571,345 bp (20.12%) number of T's = 91,378,526 bp (30.36%) number of G's = 58,788,099 bp (19.53%) number of N's = 72,414 bp (0.02%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,161,679 number of insertions = 6,692 mapped reads with insertion percentage = 0.09% number of deletions = 21,671 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0972X std coverageData = 0.8754X There is a 8.09% of reference with a coverageData >= 1X There is a 1.19% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 23996622 0.09627507407494082 2.1362516690212434 chr2 243199373 26322477 0.1082341482845846 0.5892354566168967 chr3 198022430 21924419 0.11071684657137072 0.39175511290914544 chr4 191154276 21876917 0.11444639093503721 0.4040124801972549 chr5 180915260 19978285 0.11042896547256434 0.3965933878410518 chr6 171115067 18649851 0.10899011599019506 0.4948561174408468 chr7 159138663 17021394 0.10695951366639293 0.8612784347244217 chr8 146364022 16323358 0.11152575460108632 1.5014205235640496 chr9 141213431 12637579 0.08949275511902263 0.5729313456605943 chr10 135534747 14211681 0.10485636572590495 0.71790374590948 chr11 135006516 14100534 0.10444335886721201 0.5879952119145443 chr12 133851895 13993344 0.10454348815905819 0.3976329978809953 chr13 115169878 10719120 0.0930722527986007 0.343207569224081 chr14 107349540 9307729 0.08670488015132621 0.4033205695970739 chr15 102531392 8226552 0.08023447101937327 0.3211872540533961 chr16 90354753 7663545 0.08481618006304549 0.4378000492682371 chr17 81195210 6319330 0.07782885221923806 0.3844265422138601 chr18 78077248 8543727 0.1094265899330878 1.2001664432822294 chr19 59128983 4216373 0.07130805885837746 1.5935213065479619 chr20 63025520 5810006 0.09218497522908181 0.36931336321675967 chr21 48129895 3961349 0.08230537382223668 0.39115422437328773 chr22 51304566 2484764 0.048431634720387265 0.2863260036730158 chrMT 16571 14517 0.876048518496168 1.3159728961446397 chrX 155270560 10227247 0.06586726421286818 0.3857023107204753 chrY 59373566 2524131 0.042512706748993316 0.3854104892057248