BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084826.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 = 1,784,754 number of mapped reads = 1,649,423 (92.42%) number of supplementary alignments = 14,249 (0.8%) number of secondary alignments = 0 number of mapped bases = 111,749,634 bp number of sequenced bases = 111,706,290 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,199 duplication rate = 3.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7722 >>>>>>> ACTG content number of A's = 31,312,018 bp (28.03%) number of C's = 20,339,228 bp (18.21%) number of T's = 35,878,779 bp (32.12%) number of G's = 24,160,290 bp (21.63%) number of N's = 15,975 bp (0.01%) GC percentage = 39.84% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 850,633 number of insertions = 9,002 mapped reads with insertion percentage = 0.54% number of deletions = 26,366 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.37% >>>>>>> Coverage mean coverageData = 0.0361X std coverageData = 0.2547X There is a 3.05% of reference with a coverageData >= 1X There is a 0.43% 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 10508392 0.04215994310401337 0.29722345873063 chr2 243199373 9510787 0.03910695526340851 0.353074052571032 chr3 198022430 7681200 0.038789545204550815 0.2277477892596412 chr4 191154276 6812353 0.0356379838450488 0.21879100668602144 chr5 180915260 5705492 0.03153682005597538 0.20454186322154502 chr6 171115067 5897477 0.03446497788531971 0.2243954498490385 chr7 159138663 6345080 0.039871391906817766 0.27856698844120753 chr8 146364022 6514401 0.04450821254420024 0.32832966679090037 chr9 141213431 7240454 0.05127312571280844 0.2995792656349749 chr10 135534747 3640215 0.02685816796485406 0.19402358956003615 chr11 135006516 4570709 0.03385546961303705 0.22991200030999065 chr12 133851895 4551975 0.0340075499117887 0.2124955517838005 chr13 115169878 2649411 0.023004374459787133 0.17399644335328776 chr14 107349540 2463944 0.022952534309881534 0.17789906944748446 chr15 102531392 3289685 0.032084661446905936 0.2115157671300689 chr16 90354753 1988446 0.02200709906207148 0.17653688959157168 chr17 81195210 3087046 0.03802005069018234 0.22787533789375478 chr18 78077248 4997663 0.06400921046807387 0.43162609486954645 chr19 59128983 2002855 0.0338726441481329 0.23692115077304587 chr20 63025520 2250057 0.03570072884761601 0.22077524651686425 chr21 48129895 947404 0.019684314707106673 0.1643525320605737 chr22 51304566 998821 0.01946846212479412 0.1576708007298987 chrMT 16571 35075 2.1166495685233238 1.8011391113154775 chrX 155270560 7837482 0.05047629119132436 0.2652842392043188 chrY 59373566 223210 0.003759417111648642 0.07962757612806057