BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231855.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 = 5,232,519 number of mapped reads = 4,887,808 (93.41%) number of supplementary alignments = 30,621 (0.59%) number of secondary alignments = 0 number of mapped bases = 313,758,504 bp number of sequenced bases = 313,640,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 481,166 duplication rate = 7.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.508 >>>>>>> ACTG content number of A's = 80,707,840 bp (25.73%) number of C's = 56,164,722 bp (17.91%) number of T's = 102,817,742 bp (32.78%) number of G's = 73,828,788 bp (23.54%) number of N's = 121,541 bp (0.04%) GC percentage = 41.45% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,988,650 number of insertions = 20,169 mapped reads with insertion percentage = 0.41% number of deletions = 68,735 mapped reads with deletion percentage = 1.39% homopolymer indels = 43.45% >>>>>>> Coverage mean coverageData = 0.1014X std coverageData = 1.0361X There is a 7.71% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.4% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 0.01% 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 32699068 0.13118951466925333 1.8375615531033633 chr2 243199373 18263439 0.07509657107545256 2.1807979318943147 chr3 198022430 34715058 0.17530871629037176 0.5383855884595158 chr4 191154276 10518295 0.05502516197963576 0.3990891717473967 chr5 180915260 18199023 0.10059418426063119 0.4089134581848238 chr6 171115067 18522554 0.10824618968240828 0.7523541454108964 chr7 159138663 21290110 0.13378339115492002 1.3329078807821098 chr8 146364022 22394156 0.15300314718052774 1.1639635033469873 chr9 141213431 11244943 0.07963083199925933 0.6317249309776334 chr10 135534747 12834120 0.09469247026373244 0.645079109168305 chr11 135006516 12686010 0.0939659090232356 0.6874762626389732 chr12 133851895 9936204 0.07423282277774251 0.3657758167579542 chr13 115169878 13341723 0.1158438580615671 0.5104690407228145 chr14 107349540 15024515 0.13995882050356248 0.5252459621378832 chr15 102531392 5558102 0.05420878319880803 0.42345095374876873 chr16 90354753 10747608 0.11894900537219111 0.5249500542005796 chr17 81195210 9172521 0.11296874532376971 0.5180095317443703 chr18 78077248 5902520 0.0755984637163441 1.4737877414326206 chr19 59128983 7331640 0.12399401491481767 1.141441958796651 chr20 63025520 9565818 0.15177689926239402 0.5508106928855117 chr21 48129895 5353461 0.11122943442947465 0.44587596570747273 chr22 51304566 2103915 0.04100833832216805 0.2437839144803401 chrMT 16571 170751 10.304206143262325 6.7133044712113925 chrX 155270560 5600711 0.03607065627894947 0.37327104302346625 chrY 59373566 582239 0.009806367365571406 0.2013507509799959