BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082512.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 = 2,819,107 number of mapped reads = 2,542,321 (90.18%) number of supplementary alignments = 30,152 (1.07%) number of secondary alignments = 0 number of mapped bases = 172,387,167 bp number of sequenced bases = 172,322,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 176,248 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8379 >>>>>>> ACTG content number of A's = 49,238,842 bp (28.57%) number of C's = 32,707,276 bp (18.98%) number of T's = 53,459,464 bp (31.02%) number of G's = 36,913,550 bp (21.42%) number of N's = 3,469 bp (0%) GC percentage = 40.4% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,446,818 number of insertions = 14,087 mapped reads with insertion percentage = 0.55% number of deletions = 39,934 mapped reads with deletion percentage = 1.55% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.0557X std coverageData = 0.5309X There is a 3.94% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% 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 13691979 0.05493257727931598 0.64745633567367 chr2 243199373 14226692 0.05849806199952662 0.532556703369675 chr3 198022430 12070301 0.060954211096187434 0.33023059412522215 chr4 191154276 11593224 0.06064852036059083 0.34676952131868316 chr5 180915260 11235678 0.062104645014467 0.3356995529759009 chr6 171115067 10139817 0.05925730081968761 0.3642335323908017 chr7 159138663 8209144 0.05158484962262125 0.38746842733450154 chr8 146364022 8643722 0.0590563301136942 1.4310430279879092 chr9 141213431 7515324 0.05321961195036753 0.4748335354912426 chr10 135534747 8207098 0.06055346087745307 0.40006301945626876 chr11 135006516 6949600 0.05147603394194692 0.4184314963587672 chr12 133851895 7463960 0.05576282651807059 0.3200300507325445 chr13 115169878 6397370 0.055547249950199655 0.3162123568784142 chr14 107349540 5253310 0.048936492881105964 0.3368133295831728 chr15 102531392 5012177 0.048884316327237616 0.29966713310472026 chr16 90354753 4658312 0.05155580470680939 0.33616311369606117 chr17 81195210 4533764 0.055837825901306246 0.3278774773591207 chr18 78077248 4962500 0.06355884879549033 1.0827329265436068 chr19 59128983 2771342 0.046869434571536604 0.46139986408722417 chr20 63025520 3021229 0.04793659774643668 0.31908331232256887 chr21 48129895 2716434 0.05643964110040132 0.3565304880688741 chr22 51304566 2131076 0.04153774539287595 0.26558044903246564 chrMT 16571 68463 4.131494780037415 3.580328353850957 chrX 155270560 10440231 0.06723896017377666 0.38246188522396596 chrY 59373566 474420 0.00799042456031696 0.15730039423360603