BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068079.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 = 2,752,461 number of mapped reads = 2,355,773 (85.59%) number of supplementary alignments = 23,385 (0.85%) number of secondary alignments = 0 number of mapped bases = 151,521,884 bp number of sequenced bases = 151,456,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,787 duplication rate = 6.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2829 >>>>>>> ACTG content number of A's = 39,435,152 bp (26.04%) number of C's = 28,059,800 bp (18.53%) number of T's = 47,969,263 bp (31.67%) number of G's = 35,989,518 bp (23.76%) number of N's = 2,919 bp (0%) GC percentage = 42.29% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,222,721 number of insertions = 11,111 mapped reads with insertion percentage = 0.47% number of deletions = 41,102 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0489X std coverageData = 0.4806X There is a 3.86% of reference with a coverageData >= 1X There is a 0.74% 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% 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 15858555 0.06362493676595493 1.0206765335014254 chr2 243199373 16468501 0.06771605040281087 0.8009277541790549 chr3 198022430 10430653 0.05267409858570062 0.2804060946691336 chr4 191154276 5039870 0.026365457814817597 0.2213271139273757 chr5 180915260 5228228 0.028898767301332125 0.20877727412028185 chr6 171115067 12464569 0.07284319971659772 0.37278979524456674 chr7 159138663 14845285 0.09328521881574435 0.6187929726320752 chr8 146364022 6076031 0.04151314590138825 0.3546269902187436 chr9 141213431 6239438 0.04418445154837999 0.38063474478464715 chr10 135534747 4107440 0.030305438944007473 0.26161091227660493 chr11 135006516 6852685 0.050758179701489374 0.31955706749420426 chr12 133851895 5261534 0.0393086254027259 0.25077330724541436 chr13 115169878 4573365 0.039709732088107276 0.24625616771654102 chr14 107349540 3523310 0.03282091381108852 0.24127018885357981 chr15 102531392 6036135 0.05887109188959416 0.3038497818780786 chr16 90354753 1870545 0.02070223134802881 0.19621497560989926 chr17 81195210 5242570 0.06456747879585507 0.3219080650110842 chr18 78077248 3032029 0.038833707356078946 0.5606709634101246 chr19 59128983 5707469 0.09652574271402571 0.6764669843836539 chr20 63025520 2578176 0.04090685804734336 0.2525055233160899 chr21 48129895 2163027 0.044941444397499725 0.2708398700966645 chr22 51304566 2394445 0.04667118712201951 0.2613789963786497 chrMT 16571 78067 4.7110614929696455 4.20535088593207 chrX 155270560 5086005 0.032755758722065535 0.23996460377713363 chrY 59373566 363952 0.006129865940678045 0.23532537947237095