BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548916.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 = 7,513,729 number of mapped reads = 6,595,325 (87.78%) number of secondary alignments = 0 number of mapped bases = 260,954,862 bp number of sequenced bases = 260,926,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,088 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1778 >>>>>>> ACTG content number of A's = 76,238,812 bp (29.22%) number of C's = 54,039,165 bp (20.71%) number of T's = 76,644,737 bp (29.37%) number of G's = 54,001,202 bp (20.7%) number of N's = 2,635 bp (0%) GC percentage = 41.41% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 755,553 number of insertions = 8,868 mapped reads with insertion percentage = 0.13% number of deletions = 21,559 mapped reads with deletion percentage = 0.33% homopolymer indels = 40.79% >>>>>>> Coverage mean coverageData = 0.0843X std coverageData = 0.9639X There is a 7.11% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.16% 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% 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 20445038 0.08202602632632959 0.9345274089593361 chr2 243199373 22009027 0.09049787722931342 0.5252155266564673 chr3 198022430 17707105 0.0894196935165375 0.34139588816911876 chr4 191154276 17386946 0.09095766186260987 0.357643456863514 chr5 180915260 16343123 0.09033579035842526 0.3512420905468996 chr6 171115067 15283081 0.08931464229272107 0.382529917822608 chr7 159138663 14581997 0.09163076228684917 0.7647489940965468 chr8 146364022 13612182 0.09300224067359941 3.747982981753783 chr9 141213431 10920157 0.07733086663689943 0.511141228337142 chr10 135534747 11939008 0.08808817122003408 0.46053953455615554 chr11 135006516 11838426 0.08768781204604968 0.5416999462288722 chr12 133851895 11915418 0.08901941956070178 0.35513827529886355 chr13 115169878 8648895 0.0750968495425514 0.30859046023425113 chr14 107349540 8004091 0.07456101814688726 0.3733474063979236 chr15 102531392 7417811 0.07234673064811215 0.30713417465744325 chr16 90354753 7027217 0.07777362857712643 0.3592883334665961 chr17 81195210 6682989 0.08230767553898807 0.356898963601755 chr18 78077248 6926026 0.08870735300506494 0.9505362693159101 chr19 59128983 5076184 0.08584933720236657 0.8865650189376495 chr20 63025520 5142998 0.08160183366991657 0.3412988529425761 chr21 48129895 3287409 0.06830285002699465 0.3374794620669772 chr22 51304566 2829059 0.05514244092816222 0.31536049836181623 chrMT 16571 8477 0.5115563333534487 0.9147652286026354 chrX 155270560 15083761 0.09714501577118032 0.4390289615255323 chrY 59373566 838437 0.014121385264277373 0.18607032590950748