BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975317.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 47,595,698 number of mapped reads = 47,386,726 (99.56%) number of supplementary alignments = 224,418 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,765,890 number of mapped paired reads (second in pair) = 23,620,836 number of mapped paired reads (both in pair) = 47,211,764 number of mapped paired reads (singletons) = 174,962 number of mapped bases = 4,629,942,472 bp number of sequenced bases = 4,629,367,474 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,592,835 duplication rate = 53.15% >>>>>>> Insert size mean insert size = 141,084.0173 std insert size = 3,702,702.4397 median insert size = 247 >>>>>>> Mapping quality mean mapping quality = 56.3987 >>>>>>> ACTG content number of A's = 1,221,112,260 bp (26.38%) number of C's = 1,083,371,044 bp (23.4%) number of T's = 1,256,298,581 bp (27.14%) number of G's = 1,067,574,635 bp (23.06%) number of N's = 1,010,954 bp (0.02%) GC percentage = 46.46% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 25,292,721 number of insertions = 371,577 mapped reads with insertion percentage = 0.78% number of deletions = 276,271 mapped reads with deletion percentage = 0.57% homopolymer indels = 35.12% >>>>>>> Coverage mean coverageData = 1.4956X std coverageData = 11.0086X There is a 10.08% of reference with a coverageData >= 1X There is a 6.93% of reference with a coverageData >= 2X There is a 4.67% of reference with a coverageData >= 3X There is a 4.08% of reference with a coverageData >= 4X There is a 3.67% of reference with a coverageData >= 5X There is a 3.44% of reference with a coverageData >= 6X There is a 3.25% of reference with a coverageData >= 7X There is a 3.1% of reference with a coverageData >= 8X There is a 2.96% of reference with a coverageData >= 9X There is a 2.84% of reference with a coverageData >= 10X There is a 2.73% of reference with a coverageData >= 11X There is a 2.63% of reference with a coverageData >= 12X There is a 2.54% of reference with a coverageData >= 13X There is a 2.45% of reference with a coverageData >= 14X There is a 2.37% of reference with a coverageData >= 15X There is a 2.29% of reference with a coverageData >= 16X There is a 2.22% of reference with a coverageData >= 17X There is a 2.15% of reference with a coverageData >= 18X There is a 2.08% of reference with a coverageData >= 19X There is a 2.02% of reference with a coverageData >= 20X There is a 1.95% of reference with a coverageData >= 21X There is a 1.9% of reference with a coverageData >= 22X There is a 1.84% of reference with a coverageData >= 23X There is a 1.79% of reference with a coverageData >= 24X There is a 1.74% of reference with a coverageData >= 25X There is a 1.69% of reference with a coverageData >= 26X There is a 1.64% of reference with a coverageData >= 27X There is a 1.59% of reference with a coverageData >= 28X There is a 1.55% of reference with a coverageData >= 29X There is a 1.51% of reference with a coverageData >= 30X There is a 1.47% of reference with a coverageData >= 31X There is a 1.43% of reference with a coverageData >= 32X There is a 1.39% of reference with a coverageData >= 33X There is a 1.35% of reference with a coverageData >= 34X There is a 1.31% of reference with a coverageData >= 35X There is a 1.28% of reference with a coverageData >= 36X There is a 1.25% of reference with a coverageData >= 37X There is a 1.21% of reference with a coverageData >= 38X There is a 1.18% of reference with a coverageData >= 39X There is a 1.15% of reference with a coverageData >= 40X There is a 1.12% of reference with a coverageData >= 41X There is a 1.09% of reference with a coverageData >= 42X There is a 1.07% of reference with a coverageData >= 43X There is a 1.04% of reference with a coverageData >= 44X There is a 1.01% of reference with a coverageData >= 45X There is a 0.99% of reference with a coverageData >= 46X There is a 0.96% of reference with a coverageData >= 47X There is a 0.94% of reference with a coverageData >= 48X There is a 0.91% of reference with a coverageData >= 49X There is a 0.89% of reference with a coverageData >= 50X There is a 0.87% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 471069244 1.8899421077069252 12.721081023205665 chr2 243199373 374785833 1.5410641416415165 11.244697526719342 chr3 198022430 298844048 1.509142413816455 11.026128408067711 chr4 191154276 215851641 1.1292012165084917 9.783552825323982 chr5 180915260 236935182 1.309647301172936 10.37411677241269 chr6 171115067 269362065 1.5741574936823068 11.901998044406424 chr7 159138663 227460651 1.4293236270308491 11.051733650650556 chr8 146364022 173738661 1.1870312022444969 9.641678649755127 chr9 141213431 186979908 1.3240943632337636 10.21610310586028 chr10 135534747 201013174 1.483111736653037 11.087798957702141 chr11 135006516 269498380 1.9961879469580563 13.058742646053954 chr12 133851895 253598089 1.8946170989958715 12.36687444066508 chr13 115169878 102207573 0.8874505623770826 8.585182722592455 chr14 107349540 155692910 1.4503360703734733 11.002791139157356 chr15 102531392 167392776 1.6326002479318724 11.617017186081851 chr16 90354753 161631414 1.788853476252655 11.497424082975389 chr17 81195210 233097097 2.870823254228913 14.977770073497165 chr18 78077248 82348381 1.0547039388478447 9.17074461952378 chr19 59128983 205218203 3.470687175526087 15.481191189633947 chr20 63025520 109430123 1.7362827470523052 11.554523182785191 chr21 48129895 50832462 1.0561515249513842 9.666482252083787 chr22 51304566 80796775 1.5748456969697395 10.208382417845854 chrMT 16571 360242 21.739303602679378 32.932438355133435 chrX 155270560 95899005 0.617625163456614 5.418705331179642 chrY 59373566 5898635 0.09934783098593067 1.6020884712000711