BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054592.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 7,294,577 number of mapped reads = 5,745,514 (78.76%) number of supplementary alignments = 129 (0%) number of secondary alignments = 0 number of mapped bases = 266,319,887 bp number of sequenced bases = 266,267,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,840,528 duplication rate = 21.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6905 >>>>>>> ACTG content number of A's = 83,507,412 bp (31.36%) number of C's = 54,924,349 bp (20.63%) number of T's = 73,046,449 bp (27.43%) number of G's = 54,788,596 bp (20.58%) number of N's = 952 bp (0%) GC percentage = 41.2% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,487,619 number of insertions = 11,380 mapped reads with insertion percentage = 0.2% number of deletions = 35,240 mapped reads with deletion percentage = 0.61% homopolymer indels = 41.67% >>>>>>> Coverage mean coverageData = 0.086X std coverageData = 0.9135X There is a 3.24% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.58% of reference with a coverageData >= 4X There is a 0.42% of reference with a coverageData >= 5X There is a 0.32% of reference with a coverageData >= 6X There is a 0.25% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% 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 24193331 0.0970642757194976 0.9921613611872366 chr2 243199373 21774603 0.0895339602705308 0.9310380417071107 chr3 198022430 19413595 0.09803735364726107 0.9625001772791348 chr4 191154276 15426299 0.0807007790921716 0.8844312308281223 chr5 180915260 13040987 0.07208339970879184 0.7657963352171862 chr6 171115067 13136450 0.07676968621354659 0.907547177771042 chr7 159138663 17175868 0.10793020172602556 1.0592714992800456 chr8 146364022 15805269 0.10798602541818644 1.0346135329626083 chr9 141213431 12971464 0.0918571548622737 0.9746184143400864 chr10 135534747 11761739 0.08678024831521618 0.8831189726961887 chr11 135006516 11889190 0.08806382352685851 0.9503843300799211 chr12 133851895 9692715 0.07241373011566254 0.7690466258566416 chr13 115169878 8435622 0.07324503721363672 0.7979347054950348 chr14 107349540 6086078 0.05669402961577665 0.7147767086640792 chr15 102531392 6974241 0.06802054340586734 0.7536290260008975 chr16 90354753 7410497 0.0820155747645063 0.928443962361947 chr17 81195210 5139593 0.06329921432557413 0.7095308692453172 chr18 78077248 9751725 0.12489842111238347 1.1226787183467604 chr19 59128983 5127420 0.08671584965362926 0.8788463678779115 chr20 63025520 4562651 0.072393706549347 0.8307883432575115 chr21 48129895 3187172 0.06622021510747114 0.9408352392024406 chr22 51304566 2624183 0.05114911214725021 0.6206431360239585 chrMT 16571 17443 1.0526220505702735 3.6054694203214153 chrX 155270560 20053044 0.12914904151823758 1.159667065926229 chrY 59373566 668708 0.011262722538848349 0.29627974149151765