BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082441.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 = 2,998,024 number of mapped reads = 2,740,969 (91.43%) number of supplementary alignments = 27,090 (0.9%) number of secondary alignments = 0 number of mapped bases = 187,076,060 bp number of sequenced bases = 187,008,747 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 107,757 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6568 >>>>>>> ACTG content number of A's = 53,250,241 bp (28.47%) number of C's = 35,247,968 bp (18.85%) number of T's = 58,099,871 bp (31.07%) number of G's = 40,406,768 bp (21.61%) number of N's = 3,899 bp (0%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,532,471 number of insertions = 14,746 mapped reads with insertion percentage = 0.53% number of deletions = 41,622 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.56% >>>>>>> Coverage mean coverageData = 0.0604X std coverageData = 0.5063X There is a 5.2% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 14789073 0.05933414705514415 0.9581476941256757 chr2 243199373 16075045 0.06609821728446644 0.586343041706334 chr3 198022430 12913890 0.06521427900869614 0.28477497446549493 chr4 191154276 12621032 0.06602537104636885 0.2998508269820469 chr5 180915260 11803586 0.06524372791991123 0.2886707836025106 chr6 171115067 11147644 0.06514706270722495 0.3525886821298394 chr7 159138663 10316145 0.06482488168195807 0.6318488514964472 chr8 146364022 9492633 0.06485632787543923 0.8610227312797499 chr9 141213431 7861511 0.055671128052968276 0.4437895808419669 chr10 135534747 8623081 0.06362265906616552 0.43704504578326253 chr11 135006516 8391040 0.06215285194086484 0.4064819046923581 chr12 133851895 8530550 0.06373126058469325 0.2889749013998954 chr13 115169878 6229303 0.05408795344907807 0.2602037215891179 chr14 107349540 5706596 0.05315901679690477 0.28274121630321764 chr15 102531392 5275642 0.05145391959566881 0.2599872994963853 chr16 90354753 4871977 0.05392053918845863 0.30084727649065846 chr17 81195210 4625239 0.05696443176881986 0.3020169786067772 chr18 78077248 5082842 0.06510016848954513 0.8412113482225712 chr19 59128983 3277605 0.05543144552308637 0.6781791139910612 chr20 63025520 3606087 0.05721629904838548 0.27535923609864216 chr21 48129895 2470911 0.051338383347813245 0.27436341409499704 chr22 51304566 1871953 0.03648706432873831 0.2117612896664986 chrMT 16571 15445 0.9320499668094865 1.1737087428525868 chrX 155270560 11031931 0.07104972764959436 0.34360687752344615 chrY 59373566 445299 0.00749995376730446 0.15723276340536935