BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080701.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 = 2,661,024 number of mapped reads = 2,340,760 (87.96%) number of supplementary alignments = 27,577 (1.04%) number of secondary alignments = 0 number of mapped bases = 165,639,233 bp number of sequenced bases = 165,574,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,173 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.961 >>>>>>> ACTG content number of A's = 50,750,563 bp (30.65%) number of C's = 30,899,027 bp (18.66%) number of T's = 50,738,681 bp (30.64%) number of G's = 33,183,433 bp (20.04%) number of N's = 2,572 bp (0%) GC percentage = 38.7% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,403,846 number of insertions = 13,223 mapped reads with insertion percentage = 0.56% number of deletions = 35,709 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.2% >>>>>>> Coverage mean coverageData = 0.0535X std coverageData = 0.6184X There is a 3.64% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.12% of reference with a coverageData >= 4X There is a 0.04% 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% 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 11941348 0.04790899999402609 0.5969038029892838 chr2 243199373 14191626 0.05835387577253334 0.4232334311025093 chr3 198022430 11222299 0.056671857829438815 0.3271957243275974 chr4 191154276 11703300 0.061224369367494556 0.36963952526836374 chr5 180915260 10463544 0.05783671316615304 0.3322426258102297 chr6 171115067 10501299 0.06136980912382192 0.3696912025972944 chr7 159138663 9455305 0.05941551111309764 0.658617134932506 chr8 146364022 9158177 0.06257123079058322 2.1016579380386786 chr9 141213431 6680790 0.04730987663630947 0.3890499089123693 chr10 135534747 8026997 0.05922464296185243 0.48648747076602267 chr11 135006516 7744596 0.05736460897931771 0.38978807342199595 chr12 133851895 7227438 0.053995783922222394 0.32223448128884835 chr13 115169878 5899324 0.05122280324027086 0.3113740917746491 chr14 107349540 5115017 0.04764824329941237 0.3266620216326581 chr15 102531392 4172543 0.040695273112063085 0.2720679107727359 chr16 90354753 4192787 0.04640361310046412 0.3210842343229314 chr17 81195210 3611623 0.04448073968895456 0.3098058605670017 chr18 78077248 4326431 0.05541218614672484 0.699670220543687 chr19 59128983 2554220 0.04319742823921054 0.46358043816802286 chr20 63025520 3105834 0.049278990478777485 0.30868046567813195 chr21 48129895 2111047 0.04386145035221872 0.3111290423879914 chr22 51304566 1432220 0.027916033828256144 0.21988799885367277 chrMT 16571 545920 32.944300283628024 18.0449953430549 chrX 155270560 9813935 0.06320538162546718 0.3567549808329747 chrY 59373566 441613 0.007437872267938227 0.21177102835884948