BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013209.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 8,466,736 number of mapped reads = 7,538,257 (89.03%) number of supplementary alignments = 43,251 (0.51%) number of secondary alignments = 0 number of mapped bases = 512,662,473 bp number of sequenced bases = 512,452,639 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 598,961 duplication rate = 5.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6969 >>>>>>> ACTG content number of A's = 145,592,034 bp (28.41%) number of C's = 93,797,470 bp (18.3%) number of T's = 163,208,798 bp (31.85%) number of G's = 109,740,589 bp (21.41%) number of N's = 113,748 bp (0.02%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 4,077,920 number of insertions = 40,174 mapped reads with insertion percentage = 0.53% number of deletions = 120,766 mapped reads with deletion percentage = 1.58% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.1656X std coverageData = 1.5386X There is a 11.33% of reference with a coverageData >= 1X There is a 3.25% of reference with a coverageData >= 2X There is a 1% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.12% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 39526313 0.15858059988544623 2.997998721013295 chr2 243199373 44648494 0.18358803087868159 1.7418260546417166 chr3 198022430 33812932 0.17075304045102366 0.562175152500619 chr4 191154276 35421873 0.1853051563439784 0.7526922746056985 chr5 180915260 32073485 0.1772845751099161 0.5879893446531402 chr6 171115067 28826982 0.16846548059967156 0.8137272670151952 chr7 159138663 28970856 0.1820478785849797 2.4514245926074802 chr8 146364022 26612833 0.18182633024391745 2.595017264192936 chr9 141213431 22073765 0.1563149117168607 1.3938528773121848 chr10 135534747 23738795 0.17514914459537081 1.290848104808097 chr11 135006516 23145657 0.17144103622376272 1.019642438150792 chr12 133851895 22695356 0.16955573172871405 0.6094998611735007 chr13 115169878 17303405 0.1502424531525509 0.5284670341180155 chr14 107349540 15987856 0.14893269221274724 0.640809409489152 chr15 102531392 14292956 0.13940077981190385 0.5193558481717422 chr16 90354753 13432897 0.14866840485967572 0.7354392345480667 chr17 81195210 11876700 0.14627340701501973 0.680966921175768 chr18 78077248 14258949 0.18262617299216283 3.0056093292768544 chr19 59128983 8603351 0.14550142017494197 2.0970497466912374 chr20 63025520 9708539 0.15404139466044867 0.5981200234283662 chr21 48129895 6930194 0.14398938539134565 0.6712211076161442 chr22 51304566 5006956 0.09759279515199486 0.40655151155253477 chrMT 16571 601287 36.28549876289904 21.729506637110617 chrX 155270560 31699877 0.2041589661298317 0.8513734070163039 chrY 59373566 1412165 0.023784406009906833 0.5561810083033046