BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013362.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,036,938 number of mapped reads = 1,772,664 (87.03%) number of supplementary alignments = 15,712 (0.77%) number of secondary alignments = 0 number of mapped bases = 119,550,473 bp number of sequenced bases = 119,500,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,708 duplication rate = 4.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9865 >>>>>>> ACTG content number of A's = 33,761,068 bp (28.25%) number of C's = 21,864,955 bp (18.3%) number of T's = 38,295,642 bp (32.05%) number of G's = 25,553,591 bp (21.38%) number of N's = 25,336 bp (0.02%) GC percentage = 39.68% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 960,468 number of insertions = 9,030 mapped reads with insertion percentage = 0.51% number of deletions = 29,061 mapped reads with deletion percentage = 1.62% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 0.0386X std coverageData = 0.3681X There is a 3.1% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.1% 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 8734620 0.035043523522454934 0.6011238151349955 chr2 243199373 14296854 0.05878655780909435 0.5304576437086205 chr3 198022430 9055852 0.04573144567511872 0.25528564511928264 chr4 191154276 6006305 0.03142124322659672 0.2539508670575099 chr5 180915260 9972990 0.05512520060496832 0.278947924091894 chr6 171115067 5728016 0.03347464428716847 0.2765151144506129 chr7 159138663 8105114 0.05093114298691827 0.5150377201373754 chr8 146364022 8777765 0.0599721494398398 0.4268539320152662 chr9 141213431 6546581 0.04635947837001425 0.3930537366277904 chr10 135534747 4151029 0.030627046509335353 0.3685353472644934 chr11 135006516 5051535 0.037416971785272944 0.27709965920710483 chr12 133851895 3600461 0.026898842186731834 0.2013105394987014 chr13 115169878 570064 0.004949766465846217 0.08338048948075111 chr14 107349540 2578227 0.024017122010955985 0.20071630735743287 chr15 102531392 1647330 0.016066591585921313 0.149644516391393 chr16 90354753 2279868 0.025232408083723054 0.21022107368819196 chr17 81195210 4716272 0.05808559396545683 0.361414296294729 chr18 78077248 3734558 0.04783157828513628 0.535524852372715 chr19 59128983 721395 0.012200362045800788 0.4965283437896417 chr20 63025520 2135819 0.033888161493947216 0.22377462644514617 chr21 48129895 1368061 0.028424350395944143 0.23364909975679699 chr22 51304566 664677 0.012955513550197462 0.1301176243768603 chrMT 16571 32735 1.9754390199746545 1.834921803676296 chrX 155270560 8813522 0.05676235082812865 0.3191427963422371 chrY 59373566 260823 0.004392914516874395 0.1508513126282696