BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080648.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,402,434 number of mapped reads = 1,258,943 (89.77%) number of supplementary alignments = 11,539 (0.82%) number of secondary alignments = 0 number of mapped bases = 82,924,526 bp number of sequenced bases = 82,893,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,561 duplication rate = 3.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4225 >>>>>>> ACTG content number of A's = 22,247,777 bp (26.84%) number of C's = 15,351,493 bp (18.52%) number of T's = 26,186,643 bp (31.59%) number of G's = 19,104,238 bp (23.05%) number of N's = 3,660 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 566,632 number of insertions = 6,026 mapped reads with insertion percentage = 0.48% number of deletions = 19,161 mapped reads with deletion percentage = 1.51% homopolymer indels = 48.22% >>>>>>> Coverage mean coverageData = 0.0268X std coverageData = 0.2266X There is a 2.34% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 10261049 0.04116759652927805 0.2611379976434693 chr2 243199373 5610789 0.023070737933193603 0.3300396457789401 chr3 198022430 5269805 0.026612162066691133 0.18700442034778483 chr4 191154276 3482709 0.018219362249578975 0.15293731578309452 chr5 180915260 3835588 0.021201019748140648 0.16199668733109032 chr6 171115067 4881275 0.028526272324108082 0.22635262315400168 chr7 159138663 5218826 0.03279420539055302 0.4155003836578337 chr8 146364022 9573585 0.06540941461693366 0.3142938443668794 chr9 141213431 2652994 0.018787122309916825 0.170533981320024 chr10 135534747 3839926 0.02833167202503429 0.1950993606155586 chr11 135006516 3570419 0.026446271674768648 0.195351417000724 chr12 133851895 2712785 0.020267064579100654 0.1647166597344374 chr13 115169878 1767273 0.015344923782935673 0.14180694916740194 chr14 107349540 1600898 0.014912946995394671 0.13869266927437854 chr15 102531392 1570296 0.015315270468580004 0.14547179421069478 chr16 90354753 2126005 0.023529531423764724 0.17696459395336953 chr17 81195210 1379758 0.016993096021304704 0.15194660850097194 chr18 78077248 2520349 0.03228019768319703 0.23210227830414204 chr19 59128983 1160523 0.019626973797266224 0.17019795112491848 chr20 63025520 2209174 0.0350520551040277 0.21344783917232515 chr21 48129895 1119090 0.023251453176866478 0.17219818083665195 chr22 51304566 815784 0.015900806957415838 0.13935273475910975 chrMT 16571 20004 1.2071691509263172 1.3677499502335428 chrX 155270560 5549597 0.035741463159532624 0.21718705023677123 chrY 59373566 176025 0.002964703181210305 0.06253269890466244