BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013211.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 = 1,866,404 number of mapped reads = 1,702,015 (91.19%) number of supplementary alignments = 10,921 (0.59%) number of secondary alignments = 0 number of mapped bases = 114,573,205 bp number of sequenced bases = 114,526,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 72,909 duplication rate = 3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8825 >>>>>>> ACTG content number of A's = 32,460,822 bp (28.34%) number of C's = 21,031,982 bp (18.36%) number of T's = 36,264,307 bp (31.66%) number of G's = 24,744,864 bp (21.61%) number of N's = 24,116 bp (0.02%) GC percentage = 39.97% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 908,552 number of insertions = 8,761 mapped reads with insertion percentage = 0.51% number of deletions = 27,274 mapped reads with deletion percentage = 1.59% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.4231X There is a 3.25% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 7793943 0.03126950283506014 0.7433297356286738 chr2 243199373 12687213 0.05216795110734106 0.48288601859046554 chr3 198022430 8724028 0.04405575671402477 0.230137717940099 chr4 191154276 8565462 0.044809157185685976 0.25569731357841774 chr5 180915260 5521213 0.030518227152314295 0.19425914568575992 chr6 171115067 8295326 0.04847805716605891 0.31236389339089493 chr7 159138663 7112702 0.04469499658923237 0.828229484476321 chr8 146364022 7799816 0.05329052791402521 0.5567869106932763 chr9 141213431 4364440 0.03090669187125692 0.3632300112075138 chr10 135534747 3876300 0.028600046008865905 0.413978778110614 chr11 135006516 3571686 0.02645565640698409 0.26613668092488746 chr12 133851895 5380334 0.040196173539418324 0.2304506087098798 chr13 115169878 2569696 0.022312222992890554 0.163398985769598 chr14 107349540 4296241 0.040021047132572714 0.24286564725471416 chr15 102531392 1944643 0.018966318139911727 0.15388965273112637 chr16 90354753 2827355 0.031291713010382534 0.22678168114923825 chr17 81195210 2860822 0.03523387648113725 0.21578956227419147 chr18 78077248 3188850 0.04084224382498727 0.7426969543166336 chr19 59128983 1912729 0.03234841701911227 0.5687649178658409 chr20 63025520 1834976 0.029114809366110744 0.1971441465132938 chr21 48129895 2210005 0.045917511351312945 0.2546674422709806 chr22 51304566 1110980 0.021654602828138143 0.15863756184000805 chrMT 16571 47767 2.8825659284291834 2.264502199182121 chrX 155270560 5827931 0.037534037360334116 0.2442112908581644 chrY 59373566 248747 0.004189524341522623 0.12435444663322207