BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708548.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,959,604 number of mapped reads = 3,258,937 (82.3%) number of supplementary alignments = 84 (0%) number of secondary alignments = 0 number of mapped bases = 162,520,838 bp number of sequenced bases = 162,505,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,010 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4688 >>>>>>> ACTG content number of A's = 50,359,307 bp (30.99%) number of C's = 30,867,550 bp (18.99%) number of T's = 50,093,915 bp (30.83%) number of G's = 31,177,816 bp (19.19%) number of N's = 7,297 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 256,510 number of insertions = 10,727 mapped reads with insertion percentage = 0.33% number of deletions = 8,702 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.52% >>>>>>> Coverage mean coverageData = 0.0525X std coverageData = 0.2358X There is a 4.98% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 12730025 0.051073192712326285 0.23375138330219877 chr2 243199373 14414403 0.05926990198284763 0.24980067755586816 chr3 198022430 13069456 0.06599987688263395 0.263641212326844 chr4 191154276 12983075 0.06791935431253444 0.26711693369730644 chr5 180915260 11226677 0.062054892439698014 0.25548783342301473 chr6 171115067 10060894 0.058796073171043434 0.2486165967252991 chr7 159138663 8735538 0.05489261902370011 0.24087106624011795 chr8 146364022 8857401 0.06051624490067648 0.25234870694148964 chr9 141213431 6569189 0.04651957645586842 0.22210727845150602 chr10 135534747 7073479 0.05218941383348729 0.23466187561160415 chr11 135006516 7453277 0.05520679461130602 0.24233873939093076 chr12 133851895 7868437 0.058784651498583564 0.2489769283684783 chr13 115169878 6017240 0.052246647339506604 0.2348534472723491 chr14 107349540 4903229 0.04567536106815176 0.22057077975432224 chr15 102531392 4143661 0.0404135837734457 0.2066408049832431 chr16 90354753 3040489 0.033650570656753385 0.18864477472679347 chr17 81195210 2608798 0.03212994953766361 0.18421284522097886 chr18 78077248 4584811 0.058721472867486316 0.24818857135207925 chr19 59128983 1350575 0.022841167418692115 0.15420487687999979 chr20 63025520 2534808 0.04021875583097133 0.20632608517256606 chr21 48129895 1959448 0.04071166163981866 0.20829088268423934 chr22 51304566 905580 0.017651060531337505 0.13607093603658893 chrMT 16571 300 0.018103916480598635 0.13332728411192565 chrX 155270560 9210323 0.05931789645120105 0.25006436148405997 chrY 59373566 219725 0.0037007209572017283 0.06307807837511063