BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617415.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 = 29,069,856 (90.84%) number of supplementary alignments = 418,136 (1.31%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,690,923 number of mapped paired reads (second in pair) = 14,378,933 number of mapped paired reads (both in pair) = 28,423,716 number of mapped paired reads (singletons) = 646,140 number of mapped bases = 2,852,128,837 bp number of sequenced bases = 2,851,502,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,275,921 duplication rate = 4.02% >>>>>>> Insert size mean insert size = 47,570.683 std insert size = 2,082,652.609 median insert size = 205 >>>>>>> Mapping quality mean mapping quality = 53.7992 >>>>>>> ACTG content number of A's = 853,766,691 bp (29.94%) number of C's = 570,716,312 bp (20.01%) number of T's = 844,369,273 bp (29.61%) number of G's = 581,640,057 bp (20.4%) number of N's = 1,010,256 bp (0.04%) GC percentage = 40.41% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 40,938,600 number of insertions = 241,325 mapped reads with insertion percentage = 0.82% number of deletions = 282,754 mapped reads with deletion percentage = 0.95% homopolymer indels = 43.67% >>>>>>> Coverage mean coverageData = 0.9213X std coverageData = 2.8105X There is a 29.12% of reference with a coverageData >= 1X There is a 16.59% of reference with a coverageData >= 2X There is a 10.55% of reference with a coverageData >= 3X There is a 7.26% of reference with a coverageData >= 4X There is a 5.25% of reference with a coverageData >= 5X There is a 3.93% of reference with a coverageData >= 6X There is a 3.03% of reference with a coverageData >= 7X There is a 2.39% of reference with a coverageData >= 8X There is a 1.92% of reference with a coverageData >= 9X There is a 1.57% of reference with a coverageData >= 10X There is a 1.29% of reference with a coverageData >= 11X There is a 1.08% of reference with a coverageData >= 12X There is a 0.91% of reference with a coverageData >= 13X There is a 0.78% of reference with a coverageData >= 14X There is a 0.67% of reference with a coverageData >= 15X There is a 0.58% of reference with a coverageData >= 16X There is a 0.5% of reference with a coverageData >= 17X There is a 0.44% of reference with a coverageData >= 18X There is a 0.38% of reference with a coverageData >= 19X There is a 0.34% of reference with a coverageData >= 20X There is a 0.3% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.19% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 183770788 0.7372932001641833 2.645949297274788 chr2 243199373 284761561 1.1708975952006258 2.9564238809780954 chr3 198022430 241128378 1.2176821484313671 3.2659221903340243 chr4 191154276 138347612 0.723748455409912 2.207435447713969 chr5 180915260 183162187 1.0124197759768856 2.7762010693188555 chr6 171115067 131408607 0.7679546243581227 2.5154262695210643 chr7 159138663 213978410 1.3446035423836633 3.126174598384949 chr8 146364022 126261105 0.862651239523877 3.1123700805130428 chr9 141213431 113978639 0.8071373819959095 2.514138599087594 chr10 135534747 91235136 0.6731494175438273 2.3122297995899537 chr11 135006516 211056419 1.5633054259395895 3.687753185801183 chr12 133851895 136072206 1.0165878189472028 2.685010041106104 chr13 115169878 124413764 1.080263052809694 2.691320036468854 chr14 107349540 82650158 0.7699162753748177 2.7757792058866886 chr15 102531392 65126427 0.6351852416087358 2.2630805392476088 chr16 90354753 71023689 0.7860537120830822 3.1769600722297993 chr17 81195210 86758994 1.0685235496034804 3.496761146439179 chr18 78077248 40926169 0.5241753525943947 1.925703913786001 chr19 59128983 39862250 0.6741575447018935 2.2132329952243155 chr20 63025520 96160185 1.525734099456855 4.49197802882573 chr21 48129895 38986700 0.8100308550434194 2.4290637007552633 chr22 51304566 22586479 0.4402430575087605 1.9779480044964788 chrMT 16571 176496 10.65089614386579 5.7889941673942875 chrX 155270560 126018692 0.8116071198558181 2.4825181968294796 chrY 59373566 2277786 0.03836363812138217 0.5443941022340036