BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084354.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 = 2,330,844 number of mapped reads = 2,142,441 (91.92%) number of supplementary alignments = 14,890 (0.64%) number of secondary alignments = 0 number of mapped bases = 144,203,726 bp number of sequenced bases = 144,155,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,143 duplication rate = 2.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7872 >>>>>>> ACTG content number of A's = 40,122,222 bp (27.83%) number of C's = 27,896,930 bp (19.35%) number of T's = 44,178,393 bp (30.65%) number of G's = 31,779,329 bp (22.05%) number of N's = 178,199 bp (0.12%) GC percentage = 41.4% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 1,376,609 number of insertions = 9,892 mapped reads with insertion percentage = 0.46% number of deletions = 28,153 mapped reads with deletion percentage = 1.3% homopolymer indels = 46.45% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.3164X There is a 3.97% of reference with a coverageData >= 1X There is a 0.52% 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% 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 13992368 0.05613774579121309 0.5014908485615635 chr2 243199373 13855560 0.056972021880993914 0.38648007661911155 chr3 198022430 9572042 0.04833817057996915 0.25193141821432263 chr4 191154276 7634643 0.0399396924816895 0.23292888905318213 chr5 180915260 7145675 0.03949735915035581 0.2246593962843589 chr6 171115067 6810491 0.03980065063469835 0.24966796333046246 chr7 159138663 7995222 0.05024060055097987 0.4364547094500523 chr8 146364022 7049872 0.04816670042040796 0.30448344272511124 chr9 141213431 5285805 0.03743131912147932 0.25963562107227744 chr10 135534747 10152428 0.07490645922702022 0.43361709110688024 chr11 135006516 7908279 0.05857701712708444 0.3250428266572627 chr12 133851895 7306618 0.05458733326113911 0.26584376526401315 chr13 115169878 3535265 0.030696090517695954 0.19771429279247482 chr14 107349540 3880625 0.03614943296450083 0.22248383547818198 chr15 102531392 3118611 0.030416157814379424 0.2002036448051811 chr16 90354753 3155260 0.03492079713836416 0.2273995151977846 chr17 81195210 4163332 0.05127558633077001 0.27090852680042604 chr18 78077248 3859139 0.049427190364086604 0.37926700378964195 chr19 59128983 3053438 0.05164029288310269 0.36860563281034936 chr20 63025520 2938564 0.04662498619606788 0.24828310266739406 chr21 48129895 1467613 0.030492752996864006 0.2065291772655186 chr22 51304566 1168830 0.022782182778819337 0.16993419614917807 chrMT 16571 11729 0.707802788003138 1.016418137268369 chrX 155270560 8838541 0.056923482468279885 0.29219554223820454 chrY 59373566 303776 0.0051163509363746145 0.10364281649121954