BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617484.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 = 29,953,673 (93.61%) number of supplementary alignments = 135,880 (0.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,162,231 number of mapped paired reads (second in pair) = 14,791,442 number of mapped paired reads (both in pair) = 29,270,134 number of mapped paired reads (singletons) = 683,539 number of mapped bases = 2,906,621,906 bp number of sequenced bases = 2,904,924,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,023,158 duplication rate = 9.75% >>>>>>> Insert size mean insert size = 31,694.3702 std insert size = 1,653,370.0372 median insert size = 218 >>>>>>> Mapping quality mean mapping quality = 52.6814 >>>>>>> ACTG content number of A's = 857,580,288 bp (29.52%) number of C's = 586,381,798 bp (20.19%) number of T's = 855,667,786 bp (29.46%) number of G's = 600,708,540 bp (20.68%) number of N's = 4,586,193 bp (0.16%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0134 number of mismatches = 38,145,513 number of insertions = 428,615 mapped reads with insertion percentage = 1.4% number of deletions = 1,002,095 mapped reads with deletion percentage = 3.28% homopolymer indels = 47.4% >>>>>>> Coverage mean coverageData = 0.9389X std coverageData = 9.4616X There is a 37.81% of reference with a coverageData >= 1X There is a 20.25% of reference with a coverageData >= 2X There is a 11.34% of reference with a coverageData >= 3X There is a 6.7% of reference with a coverageData >= 4X There is a 4.11% of reference with a coverageData >= 5X There is a 2.62% of reference with a coverageData >= 6X There is a 1.73% of reference with a coverageData >= 7X There is a 1.18% of reference with a coverageData >= 8X There is a 0.82% of reference with a coverageData >= 9X There is a 0.59% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.26% of reference with a coverageData >= 13X There is a 0.2% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.09% 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 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% 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 0.03% 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 0.02% 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 0.01% 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 187241977 0.751219701073483 9.18583207206737 chr2 243199373 300597459 1.2360124752459785 11.053642489381378 chr3 198022430 240727937 1.2156599482189971 2.202809147626115 chr4 191154276 150420669 0.7869071628824039 5.819230292092851 chr5 180915260 186225563 1.0293524327356354 2.0307773295965186 chr6 171115067 136974408 0.8004812808214019 5.325528735238933 chr7 159138663 224384728 1.4099950556955476 12.937119513599857 chr8 146364022 129178120 0.8825811031620872 3.7518404642899377 chr9 141213431 120274069 0.8517183397378115 18.05505428129533 chr10 135534747 122977019 0.9073468001530265 18.34627204422922 chr11 135006516 163901579 1.2140271733254713 12.273842259799562 chr12 133851895 126693069 0.946516812481437 1.9240387607113922 chr13 115169878 123630577 1.0734627764388185 2.080822241595449 chr14 107349540 84490656 0.7870611834945916 2.153543879926253 chr15 102531392 65676818 0.640553265871978 1.4251152564527727 chr16 90354753 78292018 0.8664958444410777 14.596067394898405 chr17 81195210 80605577 0.9927380814705695 13.118757087381308 chr18 78077248 52011229 0.6661508996833495 16.522210315340363 chr19 59128983 34600345 0.585167260529409 5.615480978349285 chr20 63025520 85590429 1.358028128923014 2.7411603042624977 chr21 48129895 41949451 0.8715882509197246 3.7270628902717426 chr22 51304566 21610549 0.42122077399504754 1.219986013826071 chrMT 16571 2000235 120.70695793856737 88.78295900827241 chrX 155270560 136631116 0.8799550668201365 4.00849348618738 chrY 59373566 9936309 0.1673524039300587 13.164997218833557