BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549083.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 = 7,790,583 number of mapped reads = 6,779,953 (87.03%) number of secondary alignments = 0 number of mapped bases = 269,309,904 bp number of sequenced bases = 269,286,028 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 210,480 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1008 >>>>>>> ACTG content number of A's = 79,793,915 bp (29.63%) number of C's = 54,922,536 bp (20.4%) number of T's = 80,955,572 bp (30.06%) number of G's = 53,550,002 bp (19.89%) number of N's = 64,003 bp (0.02%) GC percentage = 40.28% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 1,047,526 number of insertions = 6,193 mapped reads with insertion percentage = 0.09% number of deletions = 19,077 mapped reads with deletion percentage = 0.28% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 0.087X std coverageData = 0.6665X There is a 7.55% of reference with a coverageData >= 1X There is a 0.86% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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% 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 22015093 0.08832512798433509 1.6436350883236321 chr2 243199373 23415591 0.09628146121906325 0.4917773340302997 chr3 198022430 19115164 0.09653029709816206 0.35269606994378355 chr4 191154276 18810018 0.09840228737546002 0.3590831649246753 chr5 180915260 17312957 0.09569649901285275 0.3509334229437288 chr6 171115067 16452663 0.09614970375460859 0.4294849499023972 chr7 159138663 15094051 0.09484842159318631 0.6557825354348311 chr8 146364022 14340723 0.0979798368754857 0.6170216501701545 chr9 141213431 11325305 0.08019991384530555 0.48247064970398484 chr10 135534747 12935231 0.09543848560103926 0.676904531562921 chr11 135006516 12492178 0.0925301857282207 0.48743150257006507 chr12 133851895 12404081 0.0926701934253527 0.35507364462464086 chr13 115169878 9363588 0.08130240443599324 0.3104658761893727 chr14 107349540 8470081 0.07890188444216902 0.361331122371599 chr15 102531392 7695630 0.07505633006523504 0.30065784933823964 chr16 90354753 7242025 0.08015101319573083 0.41340606521776657 chr17 81195210 6466944 0.07964686586807276 0.35939305519717674 chr18 78077248 7416583 0.09499032291711922 0.9673151480353308 chr19 59128983 4429429 0.07491130026707883 1.2824862096724805 chr20 63025520 5405139 0.08576111708400026 0.3332485137845548 chr21 48129895 3521238 0.07316114028505569 0.3499991398152532 chr22 51304566 2706933 0.052762029017066434 0.2889130893267455 chrMT 16571 16098 0.9714561583489228 1.3585458447070575 chrX 155270560 8732645 0.05624147294889643 0.3346445846188508 chrY 59373566 2130516 0.03588324137377903 0.3165687796290268