BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084963.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 = 3,111,204 number of mapped reads = 2,816,778 (90.54%) number of supplementary alignments = 25,959 (0.83%) number of secondary alignments = 0 number of mapped bases = 185,737,963 bp number of sequenced bases = 185,669,479 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,765 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.784 >>>>>>> ACTG content number of A's = 51,467,835 bp (27.72%) number of C's = 34,287,810 bp (18.47%) number of T's = 57,929,883 bp (31.2%) number of G's = 41,959,434 bp (22.6%) number of N's = 24,517 bp (0.01%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,569,052 number of insertions = 14,798 mapped reads with insertion percentage = 0.52% number of deletions = 42,611 mapped reads with deletion percentage = 1.5% homopolymer indels = 46.29% >>>>>>> Coverage mean coverageData = 0.06X std coverageData = 0.5958X There is a 5.15% of reference with a coverageData >= 1X There is a 0.58% 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 0.01% 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 14792974 0.05934979796900887 1.1716975257413829 chr2 243199373 16190902 0.06657460420344094 0.7574427671952951 chr3 198022430 11879506 0.05999070913330374 0.2819148371256605 chr4 191154276 12172640 0.06367966364508634 0.3005808586640654 chr5 180915260 11393290 0.06297583741692105 0.2869696586055111 chr6 171115067 11215610 0.06554425742065133 0.43869075817789804 chr7 159138663 9689982 0.06089018103664726 0.5588546282974999 chr8 146364022 9552066 0.06526239078070703 0.8596632729841904 chr9 141213431 7982136 0.056525331503346876 0.5698153486166626 chr10 135534747 9002365 0.06642108536196994 0.5914784989713077 chr11 135006516 8283269 0.06135458676676021 0.5499663438312266 chr12 133851895 8378868 0.06259805287030117 0.29609779717626705 chr13 115169878 6148556 0.053386841305849086 0.2587890581650387 chr14 107349540 5617142 0.052325720259257746 0.32595531994855736 chr15 102531392 5273165 0.05142976114086113 0.263908921477052 chr16 90354753 5107424 0.056526345658871976 0.33801441083450967 chr17 81195210 4707167 0.05797345680859745 0.3710722799424354 chr18 78077248 5071417 0.06495383904924518 1.1451957651850204 chr19 59128983 3610254 0.06105726526701804 0.8525736653328425 chr20 63025520 3628714 0.05757531234966407 0.30019148441492927 chr21 48129895 2344438 0.04871064023721639 0.29014985928807174 chr22 51304566 1920656 0.03743635605454688 0.21477156091202804 chrMT 16571 26631 1.607084665982741 1.5774804175702464 chrX 155270560 11284870 0.07267874863077714 0.4064623136228691 chrY 59373566 463921 0.007813595026446617 0.1541293162205196