BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819148.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,984,429 number of mapped reads = 3,640,728 (91.37%) number of supplementary alignments = 16,487 (0.41%) number of secondary alignments = 0 number of mapped bases = 211,946,516 bp number of sequenced bases = 211,881,785 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 447,738 duplication rate = 8.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7922 >>>>>>> ACTG content number of A's = 50,517,323 bp (23.84%) number of C's = 37,997,738 bp (17.93%) number of T's = 69,760,727 bp (32.92%) number of G's = 53,602,880 bp (25.3%) number of N's = 3,117 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,084,420 number of insertions = 14,923 mapped reads with insertion percentage = 0.41% number of deletions = 38,149 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.0685X std coverageData = 0.6083X There is a 4.83% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.39% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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 21044040 0.08442923799174808 1.2137112290784902 chr2 243199373 16304987 0.06704370491942016 0.7853754968545471 chr3 198022430 11107161 0.05609041864600894 0.32095083202211366 chr4 191154276 12387953 0.06480604702768983 0.48237951578013816 chr5 180915260 11553327 0.0638604338849028 0.3438162233967257 chr6 171115067 9029885 0.05277083519477569 0.4072437160136272 chr7 159138663 9298017 0.058427140361233275 0.5600045685567087 chr8 146364022 19869441 0.1357535870393067 0.6802841747483125 chr9 141213431 9100568 0.06444548465081909 0.4669377113715171 chr10 135534747 11184706 0.08252279395187125 0.6922068614863691 chr11 135006516 6835997 0.05063457085286165 0.49176142178184 chr12 133851895 9939201 0.07425521319664544 0.37259566302682734 chr13 115169878 4554741 0.03954802313848071 0.27185980456805664 chr14 107349540 5266625 0.049060526947763354 0.3074531517250456 chr15 102531392 5791025 0.056480506965125375 0.3240514765848352 chr16 90354753 6690268 0.07404445010214349 0.4075412704560859 chr17 81195210 7316117 0.09010527837787476 0.44477311764101646 chr18 78077248 5094569 0.0652503658940438 0.9857554523009137 chr19 59128983 4533412 0.07666987947348934 0.8258003936703252 chr20 63025520 6125390 0.09718904342241048 0.4419957971569336 chr21 48129895 2980386 0.061923800166196086 0.4484079547383781 chr22 51304566 1784435 0.0347812122609126 0.25651965312217007 chrMT 16571 29310 1.7687526401544869 1.9858955564697915 chrX 155270560 13256270 0.08537529587064026 0.44526538900729157 chrY 59373566 868685 0.014630837568354914 0.49530840768035334