BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008768.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 = 9,080,929 number of mapped reads = 8,329,335 (91.72%) number of supplementary alignments = 68,455 (0.75%) number of secondary alignments = 0 number of mapped bases = 555,602,691 bp number of sequenced bases = 555,372,203 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,097,921 duplication rate = 9.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1612 >>>>>>> ACTG content number of A's = 151,321,043 bp (27.25%) number of C's = 102,076,143 bp (18.38%) number of T's = 176,278,671 bp (31.74%) number of G's = 125,594,244 bp (22.61%) number of N's = 102,102 bp (0.02%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 4,195,744 number of insertions = 48,200 mapped reads with insertion percentage = 0.57% number of deletions = 140,670 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.44% >>>>>>> Coverage mean coverageData = 0.1795X std coverageData = 1.845X There is a 9.51% of reference with a coverageData >= 1X There is a 4.12% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 0.88% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 49443916 0.19837028209450278 2.2665820904651537 chr2 243199373 33433482 0.13747355343716286 3.5631008178715176 chr3 198022430 28614790 0.14450277173146497 0.6886965887342258 chr4 191154276 33237041 0.17387547741804113 0.8209529195678982 chr5 180915260 49453707 0.27335287802698344 0.8754166552739073 chr6 171115067 38342019 0.22407155414315444 1.0373663608183183 chr7 159138663 18404474 0.11565055061446633 2.3649957940187023 chr8 146364022 33089719 0.22607822979885042 2.301481270317485 chr9 141213431 18717657 0.1325487021131864 2.439765674005137 chr10 135534747 48273808 0.3561729303261251 2.285833769994368 chr11 135006516 41195229 0.3051351165894837 1.371472803294832 chr12 133851895 20782551 0.15526527285997707 0.7742510262287865 chr13 115169878 3137706 0.027244154934331005 0.2566208776287564 chr14 107349540 5441535 0.050689877199287484 0.5903634054028566 chr15 102531392 5313267 0.05182088037973775 0.3917505375441693 chr16 90354753 5005119 0.055394086462723216 0.8985072413558413 chr17 81195210 41682133 0.5133570440916404 2.775336757074137 chr18 78077248 11227802 0.14380376214079676 3.226357382843371 chr19 59128983 9150440 0.1547538877846081 1.6220114934709238 chr20 63025520 25027163 0.39709570028140984 1.149618317496028 chr21 48129895 8924141 0.18541783646110177 0.8386183571386739 chr22 51304566 6179774 0.12045270980364593 0.5415610954496403 chrMT 16571 170623 10.296481805563937 6.501724514546264 chrX 155270560 19982035 0.12869171721928485 0.9928814963385573 chrY 59373566 1372560 0.023117358320704537 0.698077418325977