BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472661.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,699,962 number of mapped reads = 18,534,029 (99.11%) number of supplementary alignments = 117,950 (0.63%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,291,708 number of mapped paired reads (second in pair) = 9,242,321 number of mapped paired reads (both in pair) = 18,427,822 number of mapped paired reads (singletons) = 106,207 number of mapped bases = 1,825,264,327 bp number of sequenced bases = 1,825,017,434 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,080,851 duplication rate = 49.14% >>>>>>> Insert size mean insert size = 25,205.7112 std insert size = 1,578,601.1099 median insert size = 220 >>>>>>> Mapping quality mean mapping quality = 54.6752 >>>>>>> ACTG content number of A's = 496,916,285 bp (27.23%) number of C's = 417,248,497 bp (22.86%) number of T's = 499,219,430 bp (27.35%) number of G's = 411,287,417 bp (22.54%) number of N's = 345,805 bp (0.02%) GC percentage = 45.4% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 11,058,493 number of insertions = 112,633 mapped reads with insertion percentage = 0.6% number of deletions = 99,436 mapped reads with deletion percentage = 0.53% homopolymer indels = 47.53% >>>>>>> Coverage mean coverageData = 0.5896X std coverageData = 27.4053X There is a 3.83% of reference with a coverageData >= 1X There is a 1.75% of reference with a coverageData >= 2X There is a 0.84% of reference with a coverageData >= 3X There is a 0.62% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 174712934 0.700952853393292 31.104594846534763 chr2 243199373 158219914 0.6505769815450964 30.96557983444718 chr3 198022430 169692095 0.8569337069543081 23.551090932404538 chr4 191154276 47543795 0.24871949503237897 13.63761455868626 chr5 180915260 64016742 0.35384932150002163 19.642973605881647 chr6 171115067 131313684 0.7673998923776829 22.48690486357298 chr7 159138663 107407566 0.6749306797933825 28.001724493014855 chr8 146364022 60290104 0.41191887990069037 16.524490935911082 chr9 141213431 131352150 0.9301675419245355 27.49222202198868 chr10 135534747 42338503 0.31238117115458225 25.468164109271708 chr11 135006516 30988826 0.22953578033226188 8.372634426846476 chr12 133851895 81703519 0.6104024078254552 22.933400220763723 chr13 115169878 60147762 0.5222525459304559 23.345200900227645 chr14 107349540 27477845 0.2559661177868112 10.044083583000626 chr15 102531392 23530921 0.2294996736219089 12.15256471531997 chr16 90354753 124316241 1.3758683065626884 56.98077941239325 chr17 81195210 110791658 1.3645097783477622 63.37821852097191 chr18 78077248 11517662 0.14751623930187704 6.669138816780426 chr19 59128983 39028837 0.6600627140838867 22.215113731028712 chr20 63025520 96135225 1.5253380694042666 61.62060250645405 chr21 48129895 11501256 0.23896283172859611 12.62747422847643 chr22 51304566 25743070 0.5017695695934744 29.5152486256973 chrMT 16571 9183 0.5541608834711242 0.8737986399392307 chrX 155270560 93381287 0.6014101256542129 22.13449430923931 chrY 59373566 2103548 0.03542903250918094 3.4997095723065486