BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926905.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 29,317,546 number of mapped reads = 27,440,296 (93.6%) number of supplementary alignments = 238,620 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,801,120 number of mapped paired reads (second in pair) = 13,639,176 number of mapped paired reads (both in pair) = 27,108,136 number of mapped paired reads (singletons) = 332,160 number of mapped bases = 2,592,421,898 bp number of sequenced bases = 2,590,424,050 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,822,286 duplication rate = 5.27% >>>>>>> Insert size mean insert size = 102,717.5315 std insert size = 3,170,201.6837 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 53.4867 >>>>>>> ACTG content number of A's = 735,620,812 bp (28.4%) number of C's = 523,773,531 bp (20.22%) number of T's = 740,998,406 bp (28.61%) number of G's = 589,784,715 bp (22.77%) number of N's = 246,586 bp (0.01%) GC percentage = 42.99% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 26,961,177 number of insertions = 411,014 mapped reads with insertion percentage = 1.48% number of deletions = 1,426,878 mapped reads with deletion percentage = 5.06% homopolymer indels = 53.18% >>>>>>> Coverage mean coverageData = 0.8374X std coverageData = 3.3048X There is a 31.64% of reference with a coverageData >= 1X There is a 17.89% of reference with a coverageData >= 2X There is a 10.78% of reference with a coverageData >= 3X There is a 6.91% of reference with a coverageData >= 4X There is a 4.57% of reference with a coverageData >= 5X There is a 3.11% of reference with a coverageData >= 6X There is a 2.16% of reference with a coverageData >= 7X There is a 1.52% of reference with a coverageData >= 8X There is a 1.08% of reference with a coverageData >= 9X There is a 0.78% of reference with a coverageData >= 10X There is a 0.57% of reference with a coverageData >= 11X There is a 0.42% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.23% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 218410326 0.8762679311438907 3.04052068204742 chr2 243199373 234553464 0.9644492956813667 4.357897075518433 chr3 198022430 169746077 0.8572063124364245 1.8855037373160086 chr4 191154276 157966847 0.8263840616361624 1.955912731834051 chr5 180915260 155610954 0.8601317213373819 1.826325169514908 chr6 171115067 144556097 0.8447888285606083 1.8367608142451175 chr7 159138663 135458078 0.8511952749031202 2.198831947243847 chr8 146364022 130751154 0.8933285121120818 2.03535030394723 chr9 141213431 106194903 0.7520170160018278 3.480472174111531 chr10 135534747 134431584 0.9918606628601299 10.141890318998888 chr11 135006516 124693808 0.9236132573038178 2.2691278089786313 chr12 133851895 119728915 0.8944880085560238 1.9490103923624307 chr13 115169878 69393353 0.6025304029583152 1.5400915305869411 chr14 107349540 79336832 0.7390514388790115 1.776442500840219 chr15 102531392 80695307 0.7870302492333275 1.8897814436045826 chr16 90354753 84686815 0.9372701732691362 4.62988322167357 chr17 81195210 68484086 0.8434498291216933 2.138598767749448 chr18 78077248 64416513 0.8250356493097708 3.4152208563202726 chr19 59128983 42675088 0.7217287670921044 2.16309253991284 chr20 63025520 61294679 0.9725374578424739 2.166820255049945 chr21 48129895 30459801 0.6328665583001999 2.5952206820174535 chr22 51304566 34926375 0.6807654312873439 1.826397793054332 chrMT 16571 3177 0.19172047552953955 0.5248796161419262 chrX 155270560 140522242 0.9050153615727283 1.987916079683906 chrY 59373566 3425423 0.05769272810731968 1.2985338450789075