BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548964.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,234,225 number of mapped reads = 7,207,302 (87.53%) number of secondary alignments = 0 number of mapped bases = 284,830,853 bp number of sequenced bases = 284,801,043 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 331,572 duplication rate = 2.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.6668 >>>>>>> ACTG content number of A's = 80,357,581 bp (28.22%) number of C's = 61,180,508 bp (21.48%) number of T's = 81,871,775 bp (28.75%) number of G's = 61,390,788 bp (21.56%) number of N's = 391 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 898,317 number of insertions = 9,733 mapped reads with insertion percentage = 0.14% number of deletions = 23,009 mapped reads with deletion percentage = 0.32% homopolymer indels = 39.05% >>>>>>> Coverage mean coverageData = 0.092X std coverageData = 0.907X There is a 7.5% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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% 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 22824688 0.09157324426485582 1.5443654552845634 chr2 243199373 24528735 0.10085854538777943 0.8815697071251548 chr3 198022430 19486934 0.09840771068206769 0.37164178686765176 chr4 191154276 18926952 0.09901401316285491 0.404616671550303 chr5 180915260 17849817 0.09866396565994488 0.3888300416056419 chr6 171115067 16770623 0.0980078685882173 0.4058216791918376 chr7 159138663 16548845 0.10399009698856147 1.4561167000737523 chr8 146364022 14824030 0.10128192569072747 1.8616551670033117 chr9 141213431 12155696 0.08608031059028656 0.9207537891625915 chr10 135534747 13446744 0.09921252149458028 0.6714692660938951 chr11 135006516 13026163 0.09648543926576107 0.622909288590779 chr12 133851895 13260188 0.09906612080464008 0.42036890291206563 chr13 115169878 9137529 0.07933957349507655 0.3249747056017249 chr14 107349540 8854985 0.08248740516261178 0.5217784918296093 chr15 102531392 8009935 0.07812178147352179 0.3385214204125891 chr16 90354753 7974882 0.08826189807635244 0.46282318612477535 chr17 81195210 7604498 0.09365697804094601 0.3959500709426305 chr18 78077248 7659116 0.09809664398007471 1.7627947352465025 chr19 59128983 6170139 0.10435050100557285 1.5382989739753312 chr20 63025520 5699196 0.09042679854128931 0.3935712518804772 chr21 48129895 3624157 0.07529949940676164 0.47679701885962755 chr22 51304566 3179316 0.06196945511633409 0.4295197283677552 chrMT 16571 12309 0.742803693198962 1.1930801765981875 chrX 155270560 10757922 0.0692850080530398 0.5139587236052579 chrY 59373566 2497454 0.04206339905539782 0.3653197615396106