BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085030.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 = 1,871,102 number of mapped reads = 1,708,643 (91.32%) number of supplementary alignments = 11,475 (0.61%) number of secondary alignments = 0 number of mapped bases = 114,874,264 bp number of sequenced bases = 114,834,097 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,377 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1833 >>>>>>> ACTG content number of A's = 31,884,770 bp (27.77%) number of C's = 22,124,862 bp (19.27%) number of T's = 35,251,870 bp (30.7%) number of G's = 25,568,120 bp (22.27%) number of N's = 4,475 bp (0%) GC percentage = 41.53% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 954,341 number of insertions = 8,012 mapped reads with insertion percentage = 0.47% number of deletions = 23,404 mapped reads with deletion percentage = 1.36% homopolymer indels = 46.92% >>>>>>> Coverage mean coverageData = 0.0371X std coverageData = 0.2892X There is a 3.27% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9061067 0.03635323741079064 0.3812702557460906 chr2 243199373 11721121 0.04819552310276721 0.41719534582097506 chr3 198022430 6503603 0.03284275927732025 0.20022672145468723 chr4 191154276 6818692 0.0356711455411021 0.21091914337366816 chr5 180915260 5840848 0.032284993537858554 0.19771445359025258 chr6 171115067 7818914 0.045693895558595085 0.28474462200220724 chr7 159138663 10196623 0.06407382598155924 0.3388064931651273 chr8 146364022 7290706 0.04981214577445815 0.4127779932905482 chr9 141213431 3717603 0.026326128992645182 0.27791108013717464 chr10 135534747 8607981 0.0635112485213847 0.3494975553240782 chr11 135006516 4832010 0.03579093915733667 0.30964216562897073 chr12 133851895 4430821 0.03310241517312848 0.20365403422469777 chr13 115169878 2355386 0.020451406573513953 0.1557156630856027 chr14 107349540 3533822 0.032918836913507034 0.20851270509841652 chr15 102531392 1715777 0.016734162743055316 0.15034674398936684 chr16 90354753 3014734 0.033365527544522204 0.2120739025734219 chr17 81195210 2014643 0.024812338067725915 0.1972708953054214 chr18 78077248 2802321 0.03589164669328509 0.44797775228146364 chr19 59128983 1988873 0.03363617804825089 0.30947818017033285 chr20 63025520 2866219 0.04547711784051921 0.23869770479839658 chr21 48129895 1292710 0.026858774572435698 0.18851365270864776 chr22 51304566 726109 0.014152911848040971 0.1292790798314691 chrMT 16571 8670 0.5232031862893006 0.8490575947064626 chrX 155270560 5493141 0.03537786557863899 0.23372793845461684 chrY 59373566 221870 0.0037368481455198428 0.077913918728127