BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708587.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 = 4,561,491 number of mapped reads = 4,466,692 (97.92%) number of supplementary alignments = 112 (0%) number of secondary alignments = 0 number of mapped bases = 222,781,244 bp number of sequenced bases = 222,761,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,919 duplication rate = 0.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6224 >>>>>>> ACTG content number of A's = 69,031,167 bp (30.99%) number of C's = 42,255,710 bp (18.97%) number of T's = 68,684,721 bp (30.83%) number of G's = 42,782,549 bp (19.21%) number of N's = 7,570 bp (0%) GC percentage = 38.17% >>>>>>> Mismatches and indels general error rate = 0.0016 number of mismatches = 329,051 number of insertions = 13,919 mapped reads with insertion percentage = 0.31% number of deletions = 11,529 mapped reads with deletion percentage = 0.26% homopolymer indels = 49.04% >>>>>>> Coverage mean coverageData = 0.072X std coverageData = 0.281X There is a 6.64% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 15401212 0.06179006470760207 0.26149910303875323 chr2 243199373 18372064 0.07554322107565631 0.2866742333886771 chr3 198022430 18039789 0.09109972541999409 0.3146577166874005 chr4 191154276 15838979 0.0828596635735211 0.299841357898808 chr5 180915260 15659705 0.08655823173788657 0.3071756941962224 chr6 171115067 14787032 0.08641572165004031 0.30634700403364556 chr7 159138663 13730366 0.08627925949082531 0.30841603210549523 chr8 146364022 13826686 0.09446779209169313 0.32055352387586417 chr9 141213431 8673285 0.06141968889630619 0.25986724563837843 chr10 135534747 9746622 0.07191234879421732 0.2789166981213913 chr11 135006516 9747232 0.07219823375043616 0.28147141158958505 chr12 133851895 11376006 0.08498950276348348 0.3058005516720754 chr13 115169878 9276752 0.08054842256583791 0.2970566286149116 chr14 107349540 7428832 0.06920227138374324 0.27664435503993523 chr15 102531392 6393459 0.06235611236020282 0.2622365912977757 chr16 90354753 4787110 0.05298127482015252 0.24009752244009663 chr17 81195210 3525797 0.043423706891083845 0.21682324186627733 chr18 78077248 5926234 0.07590218856074435 0.28668706289438944 chr19 59128983 2046613 0.03461268731782517 0.1924417301716053 chr20 63025520 3547398 0.05628510482737786 0.24873638037355902 chr21 48129895 3013700 0.06261596872380461 0.2656541895505873 chr22 51304566 1378115 0.02686144932987056 0.17048323661983272 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 10003220 0.06442444723584433 0.26447545826884705 chrY 59373566 254736 0.004290394146108724 0.06867973483699043