BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238502.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 = 2,755,890 number of mapped reads = 2,343,650 (85.04%) number of supplementary alignments = 24,072 (0.87%) number of secondary alignments = 0 number of mapped bases = 142,192,060 bp number of sequenced bases = 142,113,578 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 865,939 duplication rate = 20.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5935 >>>>>>> ACTG content number of A's = 35,909,214 bp (25.27%) number of C's = 24,397,204 bp (17.17%) number of T's = 48,943,544 bp (34.44%) number of G's = 32,860,259 bp (23.12%) number of N's = 3,357 bp (0%) GC percentage = 40.29% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 953,965 number of insertions = 10,195 mapped reads with insertion percentage = 0.43% number of deletions = 47,573 mapped reads with deletion percentage = 2.01% homopolymer indels = 38.78% >>>>>>> Coverage mean coverageData = 0.0459X std coverageData = 1.117X There is a 1.48% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.41% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.23% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 17137308 0.06875532719334729 0.9206241811483586 chr2 243199373 11761919 0.04836327846947204 2.7171595053070825 chr3 198022430 4771272 0.024094603828465292 0.42139315055135973 chr4 191154276 7675001 0.04015082037714919 0.5164547719537919 chr5 180915260 7823406 0.04324348316443842 0.551891398941567 chr6 171115067 6551331 0.03828611422043858 1.0538965118192798 chr7 159138663 4667570 0.029330207455620008 0.5964204154809476 chr8 146364022 4462417 0.030488483023512432 0.9526078237025296 chr9 141213431 9761280 0.06912430305584742 0.8756298449903764 chr10 135534747 6011131 0.04435121718270518 0.5715281349561813 chr11 135006516 7211470 0.053415718097636115 0.6422051029002765 chr12 133851895 3866216 0.028884282885946442 0.48542258653879017 chr13 115169878 2458305 0.021345034332675077 0.6855911808393824 chr14 107349540 2407908 0.022430538593830956 0.5046855129750094 chr15 102531392 6823054 0.06654599988265057 0.9891340373666755 chr16 90354753 4445015 0.04919514306015534 0.6826638477046877 chr17 81195210 5525833 0.06805614518393388 0.6810916856254936 chr18 78077248 8508195 0.10897150217179785 2.9293832738970167 chr19 59128983 1909973 0.032301807051205327 0.6289691203284968 chr20 63025520 3134327 0.04973107718904977 0.6156623147950079 chr21 48129895 6433266 0.1336646589401452 0.9830038458789306 chr22 51304566 2249575 0.04384746184189532 0.5250310078975402 chrMT 16571 109743 6.622593687767787 7.504309481342814 chrX 155270560 6059918 0.039028119689914174 0.548957637635678 chrY 59373566 426627 0.007185470382560482 0.30447903281080463