BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504636.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 330,459,032 number of mapped reads = 286,827,988 (86.8%) number of supplementary alignments = 3,100,685 (0.94%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 143,935,571 number of mapped paired reads (second in pair) = 142,892,417 number of mapped paired reads (both in pair) = 284,322,010 number of mapped paired reads (singletons) = 2,505,978 number of mapped bases = 28,292,094,943 bp number of sequenced bases = 28,285,358,608 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,966,064 duplication rate = 24.72% >>>>>>> Insert size mean insert size = 39,985.0004 std insert size = 1,907,618.0551 median insert size = 366 >>>>>>> Mapping quality mean mapping quality = 53.6231 >>>>>>> ACTG content number of A's = 7,098,393,368 bp (25.1%) number of C's = 6,922,345,279 bp (24.47%) number of T's = 7,134,401,367 bp (25.22%) number of G's = 7,078,484,032 bp (25.03%) number of N's = 51,734,562 bp (0.18%) GC percentage = 49.5% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 229,546,124 number of insertions = 3,031,002 mapped reads with insertion percentage = 1.03% number of deletions = 2,699,990 mapped reads with deletion percentage = 0.91% homopolymer indels = 36.92% >>>>>>> Coverage mean coverageData = 9.1392X std coverageData = 35.8869X There is a 61.79% of reference with a coverageData >= 1X There is a 50.7% of reference with a coverageData >= 2X There is a 43.24% of reference with a coverageData >= 3X There is a 37.75% of reference with a coverageData >= 4X There is a 33.42% of reference with a coverageData >= 5X There is a 29.93% of reference with a coverageData >= 6X There is a 27.04% of reference with a coverageData >= 7X There is a 24.61% of reference with a coverageData >= 8X There is a 22.55% of reference with a coverageData >= 9X There is a 20.77% of reference with a coverageData >= 10X There is a 19.22% of reference with a coverageData >= 11X There is a 17.86% of reference with a coverageData >= 12X There is a 16.66% of reference with a coverageData >= 13X There is a 15.59% of reference with a coverageData >= 14X There is a 14.63% of reference with a coverageData >= 15X There is a 13.77% of reference with a coverageData >= 16X There is a 13% of reference with a coverageData >= 17X There is a 12.29% of reference with a coverageData >= 18X There is a 11.65% of reference with a coverageData >= 19X There is a 11.06% of reference with a coverageData >= 20X There is a 10.52% of reference with a coverageData >= 21X There is a 10.02% of reference with a coverageData >= 22X There is a 9.56% of reference with a coverageData >= 23X There is a 9.13% of reference with a coverageData >= 24X There is a 8.73% of reference with a coverageData >= 25X There is a 8.36% of reference with a coverageData >= 26X There is a 8.02% of reference with a coverageData >= 27X There is a 7.7% of reference with a coverageData >= 28X There is a 7.4% of reference with a coverageData >= 29X There is a 7.11% of reference with a coverageData >= 30X There is a 6.85% of reference with a coverageData >= 31X There is a 6.6% of reference with a coverageData >= 32X There is a 6.36% of reference with a coverageData >= 33X There is a 6.14% of reference with a coverageData >= 34X There is a 5.93% of reference with a coverageData >= 35X There is a 5.73% of reference with a coverageData >= 36X There is a 5.54% of reference with a coverageData >= 37X There is a 5.36% of reference with a coverageData >= 38X There is a 5.18% of reference with a coverageData >= 39X There is a 5.02% of reference with a coverageData >= 40X There is a 4.87% of reference with a coverageData >= 41X There is a 4.72% of reference with a coverageData >= 42X There is a 4.58% of reference with a coverageData >= 43X There is a 4.44% of reference with a coverageData >= 44X There is a 4.31% of reference with a coverageData >= 45X There is a 4.19% of reference with a coverageData >= 46X There is a 4.07% of reference with a coverageData >= 47X There is a 3.96% of reference with a coverageData >= 48X There is a 3.85% of reference with a coverageData >= 49X There is a 3.75% of reference with a coverageData >= 50X There is a 3.65% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2719119820 10.909179720759854 35.31538098426058 chr2 243199373 2294946835 9.436483353927068 27.675623819946647 chr3 198022430 1340695781 6.770423840370002 22.988027115059655 chr4 191154276 875615492 4.5806743658718885 14.25726103425765 chr5 180915260 1905762551 10.534006644878934 29.841600286915778 chr6 171115067 814733492 4.761319422561428 17.469379685366967 chr7 159138663 1948155943 12.241877028965613 31.42315283650221 chr8 146364022 1506256797 10.291168392461913 26.919018039607995 chr9 141213431 979380703 6.9354642548129855 66.21888747922229 chr10 135534747 1148507827 8.473899515966927 27.045290796365585 chr11 135006516 1322648796 9.79692562394544 33.56712218435968 chr12 133851895 1190966857 8.897646589164838 26.45644667106093 chr13 115169878 130929306 1.1368363696625605 5.304062257106139 chr14 107349540 873267777 8.134806884128242 22.01258372602371 chr15 102531392 1031045050 10.05589634440933 28.257562987882793 chr16 90354753 1831043527 20.265049332822592 50.485189721189904 chr17 81195210 1223631391 15.070241101661047 39.585748604648884 chr18 78077248 485392095 6.216818694736782 67.74509063454231 chr19 59128983 1534817570 25.957110914625403 106.73145755115401 chr20 63025520 967843278 15.356371165204191 46.20105675444557 chr21 48129895 303133841 6.298244386363195 20.605757675791928 chr22 51304566 708293262 13.805657414585673 33.99377621913391 chrMT 16571 2720561 164.17603041457969 64.26779686620111 chrX 155270560 1111316687 7.157291678474014 17.265921314423796 chrY 59373566 41869704 0.7051909935812176 31.29904723965088