BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472638.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,876,578 number of mapped reads = 15,737,603 (99.12%) number of supplementary alignments = 77,029 (0.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,886,953 number of mapped paired reads (second in pair) = 7,850,650 number of mapped paired reads (both in pair) = 15,645,104 number of mapped paired reads (singletons) = 92,499 number of mapped bases = 1,540,388,361 bp number of sequenced bases = 1,540,177,509 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,490,478 duplication rate = 49.86% >>>>>>> Insert size mean insert size = 21,095.1378 std insert size = 1,456,216.0069 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 54.7944 >>>>>>> ACTG content number of A's = 427,605,458 bp (27.76%) number of C's = 344,020,610 bp (22.34%) number of T's = 428,297,322 bp (27.81%) number of G's = 339,972,067 bp (22.07%) number of N's = 282,052 bp (0.02%) GC percentage = 44.41% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 9,539,302 number of insertions = 92,535 mapped reads with insertion percentage = 0.58% number of deletions = 80,326 mapped reads with deletion percentage = 0.5% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.4976X std coverageData = 19.8685X There is a 3.18% of reference with a coverageData >= 1X There is a 1.5% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 226680321 0.9094473670338418 27.529309768429705 chr2 243199373 136272250 0.5603314199333894 25.765041129056364 chr3 198022430 114066311 0.5760272258046727 15.516147276689555 chr4 191154276 37584583 0.19661910675751768 11.78528524745018 chr5 180915260 78423073 0.43347959149493526 16.81511093480604 chr6 171115067 123125796 0.7195497051115902 20.297576740905335 chr7 159138663 96614448 0.607108581778144 20.2074121598881 chr8 146364022 57684133 0.3941141560048138 12.970054172404115 chr9 141213431 81769020 0.5790456291654014 18.828016016818427 chr10 135534747 37432234 0.27618182664258045 12.582644690839743 chr11 135006516 39917462 0.2956706326678336 11.827898097556195 chr12 133851895 42419544 0.3169140339776288 11.433054037117747 chr13 115169878 56488894 0.490483232082611 21.48882796523717 chr14 107349540 27242297 0.25377190251583753 10.856924398223397 chr15 102531392 23814225 0.23226276885034391 12.064034930006649 chr16 90354753 87411069 0.9674208173641955 37.11146996017994 chr17 81195210 57245440 0.7050346935490407 20.6220232001646 chr18 78077248 11291311 0.14461717451926584 5.808783712555897 chr19 59128983 35158024 0.5945988281246102 16.13901733048322 chr20 63025520 60506088 0.9600252088360397 49.26471537253609 chr21 48129895 12056500 0.25049919597788445 13.827934779563959 chr22 51304566 15739863 0.3067926351818277 11.745567811104834 chrMT 16571 6814 0.4112002896626637 0.834651788402546 chrX 155270560 80175250 0.5163583489362052 18.136386133865727 chrY 59373566 1263411 0.021279014974441655 1.1246673240785707