BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971283.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,487,541 number of mapped reads = 7,949,877 (83.79%) number of secondary alignments = 0 number of mapped bases = 313,857,369 bp number of sequenced bases = 313,825,147 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 422,821 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6102 >>>>>>> ACTG content number of A's = 91,127,929 bp (29.04%) number of C's = 63,460,853 bp (20.22%) number of T's = 93,644,555 bp (29.84%) number of G's = 65,589,427 bp (20.9%) number of N's = 2,383 bp (0%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 874,065 number of insertions = 10,343 mapped reads with insertion percentage = 0.13% number of deletions = 25,229 mapped reads with deletion percentage = 0.32% homopolymer indels = 42.13% >>>>>>> Coverage mean coverageData = 0.1014X std coverageData = 0.7559X There is a 8.13% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 25771306 0.10339515262431383 1.2598288968915425 chr2 243199373 26797554 0.11018759493265634 0.5975835670340967 chr3 198022430 21656039 0.10936154555824812 0.3978895454287928 chr4 191154276 20853857 0.10909437882519563 0.41747949762646663 chr5 180915260 19790445 0.10939068932051392 0.4079664401045626 chr6 171115067 18298879 0.10693902834400901 0.4335981567437559 chr7 159138663 17407646 0.1093866548319562 1.04794845085892 chr8 146364022 16306436 0.11141013875664062 1.7940127510743007 chr9 141213431 13398200 0.09487907704756497 0.6109067278594094 chr10 135534747 14955207 0.11034223570727586 0.5749293887420369 chr11 135006516 14761566 0.10933965587260988 0.6318322730150631 chr12 133851895 14486037 0.10822436992767268 0.41583581239029577 chr13 115169878 7188007 0.062412213374056016 0.2919525431510319 chr14 107349540 9799258 0.09128365151820865 0.4840224951824612 chr15 102531392 8992977 0.08770949876502213 0.3503750709763354 chr16 90354753 8404731 0.09301924603789244 0.4026513735941738 chr17 81195210 7982120 0.09830776963320866 0.42632934296610964 chr18 78077248 8333129 0.10672928687240615 1.225143362866289 chr19 59128983 5556216 0.09396772476198348 1.1247820890731022 chr20 63025520 6440353 0.10218643178191945 0.40679547151412143 chr21 48129895 4096544 0.08511433486401747 0.4052582103936232 chr22 51304566 3505988 0.06833676363230516 0.30959917034799805 chrMT 16571 26038 1.5712992577394242 2.008773153154607 chrX 155270560 18093484 0.11652874827011638 0.526875234793432 chrY 59373566 955352 0.016090527559015067 0.21852242425828208