BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013236.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 = 1,854,656 number of mapped reads = 1,614,873 (87.07%) number of supplementary alignments = 22,318 (1.2%) number of secondary alignments = 0 number of mapped bases = 105,973,045 bp number of sequenced bases = 105,930,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,779 duplication rate = 9.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.9469 >>>>>>> ACTG content number of A's = 28,754,031 bp (27.14%) number of C's = 20,224,347 bp (19.09%) number of T's = 32,889,796 bp (31.05%) number of G's = 24,049,378 bp (22.7%) number of N's = 12,508 bp (0.01%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 790,515 number of insertions = 6,792 mapped reads with insertion percentage = 0.42% number of deletions = 24,668 mapped reads with deletion percentage = 1.51% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.0342X std coverageData = 0.3889X There is a 1.91% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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% 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 5700343 0.022869924966004398 0.560952440217182 chr2 243199373 9026393 0.03711519848367372 0.5111960896486564 chr3 198022430 4988153 0.02518983834306043 0.25461042351047114 chr4 191154276 5830949 0.030503889957449865 0.29057554712348055 chr5 180915260 4356730 0.0240816059408145 0.2497359027146775 chr6 171115067 3662212 0.021402042872121833 0.24925532205207485 chr7 159138663 7624548 0.047911348859327796 0.47345388272675654 chr8 146364022 7432348 0.050779883597350174 0.4089635629331023 chr9 141213431 5245805 0.037148059946224235 0.3600084744698707 chr10 135534747 7466875 0.05509196103048025 0.46482573926750537 chr11 135006516 7260504 0.053778915382128666 0.43287750858673935 chr12 133851895 3558573 0.026585899288164728 0.2677771125885712 chr13 115169878 4539805 0.039418336450786205 0.32566361860610193 chr14 107349540 2800675 0.0260893060184515 0.2840178367567676 chr15 102531392 3672938 0.035822570320707244 0.31090806257666037 chr16 90354753 2443666 0.02704524022106507 0.27005808693854527 chr17 81195210 2557839 0.0315023386231774 0.3436131384566113 chr18 78077248 2847737 0.03647332703119864 0.6293733109082725 chr19 59128983 2694514 0.04557010561132093 0.48892759127965285 chr20 63025520 2633231 0.04178039308521374 0.3541218677013799 chr21 48129895 1125937 0.02339371403158058 0.2542130981728899 chr22 51304566 2342911 0.04566671512239281 0.3515697503271737 chrMT 16571 3573 0.21561764528392977 0.5920539835705368 chrX 155270560 5708228 0.03676310563960097 0.3689478198319018 chrY 59373566 448558 0.0075548435140311435 0.16939306074594043