BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617492.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,524,026 (95.39%) number of supplementary alignments = 158,703 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,393,887 number of mapped paired reads (second in pair) = 15,130,139 number of mapped paired reads (both in pair) = 29,976,422 number of mapped paired reads (singletons) = 547,604 number of mapped bases = 2,971,001,623 bp number of sequenced bases = 2,969,221,326 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,298,442 duplication rate = 9.97% >>>>>>> Insert size mean insert size = 38,590.3782 std insert size = 1,840,796.9257 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 52.7278 >>>>>>> ACTG content number of A's = 875,291,277 bp (29.48%) number of C's = 600,132,892 bp (20.21%) number of T's = 875,699,307 bp (29.49%) number of G's = 614,828,516 bp (20.71%) number of N's = 3,269,334 bp (0.11%) GC percentage = 40.92% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 34,531,305 number of insertions = 445,534 mapped reads with insertion percentage = 1.43% number of deletions = 1,040,021 mapped reads with deletion percentage = 3.34% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.9597X std coverageData = 9.6261X There is a 38.23% of reference with a coverageData >= 1X There is a 20.62% of reference with a coverageData >= 2X There is a 11.64% of reference with a coverageData >= 3X There is a 6.92% of reference with a coverageData >= 4X There is a 4.27% of reference with a coverageData >= 5X There is a 2.74% of reference with a coverageData >= 6X There is a 1.81% of reference with a coverageData >= 7X There is a 1.24% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191180575 0.7670214590959835 9.425944012050948 chr2 243199373 306744715 1.2612890864648734 11.453496759484384 chr3 198022430 245525029 1.2398849413170012 2.2401940564442655 chr4 191154276 153255709 0.8017383247027129 6.1468564763074465 chr5 180915260 190309417 1.0519257303115281 2.0808588245970134 chr6 171115067 139825359 0.8171422975862201 5.353159961239624 chr7 159138663 229621638 1.4429028978331935 13.126960852397952 chr8 146364022 131659200 0.8995325367596143 3.8478015711516034 chr9 141213431 123047014 0.8713548925810038 18.11644590264268 chr10 135534747 125728507 0.9276477787648063 18.438241871389856 chr11 135006516 167694679 1.242122854277641 12.552644894864802 chr12 133851895 130119418 0.9721148736818407 2.00706370139098 chr13 115169878 126075472 1.0946913740761277 2.128559828206053 chr14 107349540 86487065 0.8056584592723919 2.1892885503380084 chr15 102531392 67044553 0.6538929365164573 1.4937422072728233 chr16 90354753 79896968 0.8842586067387069 14.562666352550993 chr17 81195210 82944888 1.0215490298011423 13.559396590882168 chr18 78077248 53075125 0.6797770971640804 16.94431941557698 chr19 59128983 35596050 0.6020068026537848 5.7182468883082 chr20 63025520 88023279 1.3966291591088815 2.7922331524687047 chr21 48129895 42766486 0.888563874905607 3.8010861242887946 chr22 51304566 22342314 0.43548392944206954 1.256094494560408 chrMT 16571 2113569 127.54625550660793 92.51421823317293 chrX 155270560 139652819 0.8994159549627437 4.138292477780889 chrY 59373566 10271775 0.17300249407286739 13.509178528001867