BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819136.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 = 1,911,501 number of mapped reads = 1,752,485 (91.68%) number of supplementary alignments = 7,621 (0.4%) number of secondary alignments = 0 number of mapped bases = 101,946,456 bp number of sequenced bases = 101,915,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,150 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6797 >>>>>>> ACTG content number of A's = 24,926,602 bp (24.46%) number of C's = 20,118,318 bp (19.74%) number of T's = 31,798,859 bp (31.2%) number of G's = 25,070,119 bp (24.6%) number of N's = 1,554 bp (0%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 525,619 number of insertions = 6,475 mapped reads with insertion percentage = 0.37% number of deletions = 18,484 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.24% >>>>>>> Coverage mean coverageData = 0.0329X std coverageData = 0.3254X There is a 2.73% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 10094471 0.04049928124351594 0.6365839583339501 chr2 243199373 7915298 0.03254653950115242 0.3934574220957008 chr3 198022430 5502715 0.027788341957019718 0.1952678642004709 chr4 191154276 5658371 0.029601069452403983 0.25027709439013685 chr5 180915260 5533546 0.030586397189490813 0.2054779140930358 chr6 171115067 4329077 0.025299215761052766 0.23224751929521473 chr7 159138663 5123721 0.03219658192051042 0.3709165010075165 chr8 146364022 9292723 0.06349048675363676 0.3576326278059037 chr9 141213431 4342947 0.030754489634912986 0.25022501383686735 chr10 135534747 5420086 0.039990379736349085 0.3608696142112707 chr11 135006516 3531024 0.026154470944202427 0.2534685974912654 chr12 133851895 4784793 0.0357469201313885 0.22310122516268588 chr13 115169878 2217206 0.019251613690169925 0.16272777498042126 chr14 107349540 2410505 0.02245473059316323 0.18013190672776494 chr15 102531392 2697958 0.026313482606380688 0.1914795614979405 chr16 90354753 3182477 0.035222020915712096 0.23206106686786152 chr17 81195210 3622873 0.04461929466036235 0.26189034190224864 chr18 78077248 2389343 0.030602295306309975 0.4659835252786142 chr19 59128983 2213970 0.037443059015576166 0.4364432625557828 chr20 63025520 2955462 0.046893099810997194 0.2584092716510747 chr21 48129895 1414870 0.029396906018598214 0.23283035480681258 chr22 51304566 855090 0.01666693759771791 0.15174615193382288 chrMT 16571 58705 3.5426347233118096 2.7381570598716154 chrX 155270560 6006932 0.03868687019612733 0.24883226999011787 chrY 59373566 392293 0.00660719957430214 0.22750771185563634