BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124959.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,564,644 number of mapped reads = 4,353,489 (95.37%) number of supplementary alignments = 20,467 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,210,902 number of mapped paired reads (second in pair) = 2,142,587 number of mapped paired reads (both in pair) = 4,260,880 number of mapped paired reads (singletons) = 92,609 number of mapped bases = 266,488,370 bp number of sequenced bases = 266,372,708 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 268,707 duplication rate = 3.45% >>>>>>> Insert size mean insert size = 99,687.1396 std insert size = 3,046,553.9009 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 51.2831 >>>>>>> ACTG content number of A's = 74,015,566 bp (27.79%) number of C's = 47,169,225 bp (17.71%) number of T's = 80,558,200 bp (30.24%) number of G's = 64,629,717 bp (24.26%) number of N's = 0 bp (0%) GC percentage = 41.97% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 1,881,365 number of insertions = 32,478 mapped reads with insertion percentage = 0.73% number of deletions = 69,583 mapped reads with deletion percentage = 1.58% homopolymer indels = 45.2% >>>>>>> Coverage mean coverageData = 0.0861X std coverageData = 1.0767X There is a 6.88% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 22185545 0.0890089858592569 0.6623679105639049 chr2 243199373 23728287 0.09756722111286036 1.1422830420246644 chr3 198022430 18377081 0.09280302741462167 0.4342634555609343 chr4 191154276 16474675 0.08618522873116372 0.7859497383082575 chr5 180915260 15834951 0.0875268951883882 0.3618304048366418 chr6 171115067 15374392 0.08984826567025801 0.4397499142861626 chr7 159138663 15639240 0.09827429554312643 0.6461886773706631 chr8 146364022 14842085 0.10140528250856622 0.42016250255419985 chr9 141213431 10862341 0.07692144382498574 0.6216192363958798 chr10 135534747 15361545 0.11334027133278228 3.941029826896432 chr11 135006516 11201907 0.08297308405469851 0.44157352555307616 chr12 133851895 12249248 0.0915134447666953 0.3560433662639653 chr13 115169878 7589255 0.06589617990217894 0.2923423273329536 chr14 107349540 8167997 0.07608786213708973 0.3806238488212427 chr15 102531392 7330787 0.07149797595647585 0.3241344187712337 chr16 90354753 9538126 0.10556307978618458 1.7912551653691224 chr17 81195210 6144604 0.07567692724730929 0.5911542595906192 chr18 78077248 6179857 0.07915054844146147 0.899490784204889 chr19 59128983 3972404 0.06718201123127722 0.5592963038412716 chr20 63025520 5502286 0.08730250857113118 0.5013247412061042 chr21 48129895 3267171 0.06788236292640988 0.48607702502687894 chr22 51304566 2506739 0.048859959170105834 0.3101330945787443 chrMT 16571 71185 4.295757648904713 3.2987744798197047 chrX 155270560 9748396 0.06278328615546952 0.372511879520305 chrY 59373566 4338266 0.07306729732217869 1.662298767740261