BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082439.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 = 3,139,269 number of mapped reads = 2,803,467 (89.3%) number of supplementary alignments = 29,185 (0.93%) number of secondary alignments = 0 number of mapped bases = 189,715,912 bp number of sequenced bases = 189,650,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,401 duplication rate = 3.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9967 >>>>>>> ACTG content number of A's = 53,649,091 bp (28.29%) number of C's = 35,507,152 bp (18.72%) number of T's = 59,396,993 bp (31.32%) number of G's = 41,093,339 bp (21.67%) number of N's = 4,071 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,541,824 number of insertions = 14,660 mapped reads with insertion percentage = 0.52% number of deletions = 40,653 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.58% >>>>>>> Coverage mean coverageData = 0.0613X std coverageData = 0.4302X There is a 5.2% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.11% 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 14907683 0.05981001347234356 0.6861576184443732 chr2 243199373 15920444 0.06546252074424551 0.5463993225107565 chr3 198022430 13012900 0.06571427287302757 0.29045600962450724 chr4 191154276 12602299 0.06592737166915377 0.30023752192555425 chr5 180915260 12145683 0.06713465188066502 0.2958495407613993 chr6 171115067 11243615 0.06570791922139738 0.34258561881517874 chr7 159138663 10564754 0.06638709789839066 0.5216479421770576 chr8 146364022 9692820 0.0662240615388391 0.719612969474614 chr9 141213431 8140895 0.0576495800884549 0.39841966895319575 chr10 135534747 8738952 0.06447757636645014 0.38412271160327943 chr11 135006516 8587042 0.06360464853414927 0.37490649633677 chr12 133851895 8697709 0.06498009609800444 0.2929028002353509 chr13 115169878 6392196 0.055502325008975006 0.267906608109456 chr14 107349540 5864914 0.05463380653517472 0.2817202300702158 chr15 102531392 5434966 0.05300782417934987 0.2670822236208894 chr16 90354753 5072527 0.056140123585972285 0.29137766153927824 chr17 81195210 4692188 0.05778897548266702 0.301106982708512 chr18 78077248 5112918 0.06548537673868833 0.6733724694433528 chr19 59128983 3454550 0.0584239712020753 0.5322557392438638 chr20 63025520 3640447 0.057761475034240096 0.27858834413720257 chr21 48129895 2483096 0.05159155240209853 0.2711725406330771 chr22 51304566 1869433 0.036437945893548734 0.21526998989820714 chrMT 16571 1328 0.0801400036207833 0.29779772955996886 chrX 155270560 11006551 0.07088627103553952 0.3370491443358845 chrY 59373566 436002 0.0073433689329018914 0.14459776695696594