BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081231.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,052,811 number of mapped reads = 1,801,387 (87.75%) number of supplementary alignments = 23,552 (1.15%) number of secondary alignments = 0 number of mapped bases = 118,013,260 bp number of sequenced bases = 117,969,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 73,810 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2662 >>>>>>> ACTG content number of A's = 33,501,357 bp (28.4%) number of C's = 22,587,138 bp (19.15%) number of T's = 36,342,531 bp (30.81%) number of G's = 25,522,843 bp (21.64%) number of N's = 15,831 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,032,072 number of insertions = 8,702 mapped reads with insertion percentage = 0.48% number of deletions = 26,748 mapped reads with deletion percentage = 1.47% homopolymer indels = 48.38% >>>>>>> Coverage mean coverageData = 0.0381X std coverageData = 0.3036X There is a 3.19% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 11484699 0.04607691228179528 0.5334425521113335 chr2 243199373 6988464 0.028735534610115958 0.3063119334886763 chr3 198022430 7194979 0.036334161741172454 0.22132929491569822 chr4 191154276 4900933 0.025638626048836072 0.19176219233350708 chr5 180915260 8694488 0.04805834510587996 0.2556908210699493 chr6 171115067 8071807 0.04717180749489465 0.27765563674244204 chr7 159138663 7894720 0.04960906326076146 0.4432480518100376 chr8 146364022 7123151 0.04866736307642598 0.37010191527111524 chr9 141213431 3311897 0.023453130318744256 0.21614058810913908 chr10 135534747 3787602 0.02794561604191433 0.24773433865656888 chr11 135006516 6467285 0.04790350267241916 0.31365755178510746 chr12 133851895 3093122 0.023108540973588755 0.17819241300227337 chr13 115169878 4080209 0.035427744396846546 0.22008322947027822 chr14 107349540 4389544 0.04089019850480961 0.24062208701703303 chr15 102531392 3616488 0.03527200723072208 0.22223131744993463 chr16 90354753 4150258 0.04593292397135987 0.25237372168625083 chr17 81195210 1990158 0.02451078086995526 0.20202312114098236 chr18 78077248 3658701 0.046860014840687005 0.34000551675789437 chr19 59128983 3243020 0.0548465377799581 0.4207988994305244 chr20 63025520 2695617 0.042770246084443256 0.24229690601056866 chr21 48129895 1642173 0.03411960487343677 0.221498121236138 chr22 51304566 886626 0.01728161972951881 0.15040677476198547 chrMT 16571 25220 1.5219359121356586 1.7024233131489468 chrX 155270560 8317662 0.053568828501681195 0.28176917442566646 chrY 59373566 304437 0.005127483836830687 0.09929531826779364