BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549062.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 = 8,841,248 number of mapped reads = 7,647,238 (86.5%) number of secondary alignments = 0 number of mapped bases = 303,713,623 bp number of sequenced bases = 303,684,527 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,764 duplication rate = 2.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4964 >>>>>>> ACTG content number of A's = 90,516,839 bp (29.81%) number of C's = 61,450,444 bp (20.23%) number of T's = 90,515,582 bp (29.81%) number of G's = 61,196,062 bp (20.15%) number of N's = 5,600 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 954,420 number of insertions = 7,638 mapped reads with insertion percentage = 0.1% number of deletions = 23,094 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.32% >>>>>>> Coverage mean coverageData = 0.0981X std coverageData = 0.9791X There is a 8.31% of reference with a coverageData >= 1X There is a 1.09% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.04% 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 0.01% 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 24626304 0.09880137470148971 2.398676435781154 chr2 243199373 26570042 0.10925209909977852 0.606280491380912 chr3 198022430 21463569 0.10838958495762324 0.3786450943112056 chr4 191154276 21378116 0.11183697507242789 0.4035243947716305 chr5 180915260 19807890 0.10948711568056779 0.38842728236125895 chr6 171115067 18729125 0.109453394890118 0.4853970432115311 chr7 159138663 17043631 0.10709924715152346 0.8895488641104676 chr8 146364022 16324060 0.11153055086174114 1.963922328034872 chr9 141213431 12754250 0.09031895839992728 0.5758710476935056 chr10 135534747 14410424 0.10632272770612838 0.755175971443556 chr11 135006516 14104855 0.10447536472980312 0.5695920846003578 chr12 133851895 14123773 0.10551791590249805 0.39922576838622587 chr13 115169878 10341410 0.08979266262659408 0.33168489495435505 chr14 107349540 9388238 0.08745485076135398 0.3893245609459762 chr15 102531392 8406801 0.08199245944110463 0.3201738181617198 chr16 90354753 7896677 0.08739636530244292 0.4237202649885793 chr17 81195210 7191027 0.08856467025579465 0.3932682287374066 chr18 78077248 8467417 0.10844922454234043 1.2556437752106597 chr19 59128983 5101263 0.08627347776301175 1.782360399382307 chr20 63025520 5933435 0.09414337239899012 0.3648148118277466 chr21 48129895 3914523 0.08133246498875595 0.38924463014944694 chr22 51304566 2887715 0.05628573098152706 0.300798613038304 chrMT 16571 17635 1.0642085571178566 1.513730383922589 chrX 155270560 10226329 0.0658613519523598 0.4085984062337437 chrY 59373566 2605114 0.043876663901238476 0.4288906157151749