BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961013.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 = 399,275,520 number of mapped reads = 384,883,279 (96.4%) number of supplementary alignments = 6,537,979 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,374,704 number of mapped paired reads (second in pair) = 187,508,575 number of mapped paired reads (both in pair) = 374,022,362 number of mapped paired reads (singletons) = 10,860,917 number of mapped bases = 37,719,501,506 bp number of sequenced bases = 37,708,560,401 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,066,989 duplication rate = 11.42% >>>>>>> Insert size mean insert size = 85,883.3019 std insert size = 2,819,380.0242 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.1448 >>>>>>> ACTG content number of A's = 11,006,080,302 bp (29.19%) number of C's = 7,793,442,677 bp (20.67%) number of T's = 10,948,089,700 bp (29.03%) number of G's = 7,857,761,373 bp (20.84%) number of N's = 103,186,349 bp (0.27%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 448,852,316 number of insertions = 3,800,276 mapped reads with insertion percentage = 0.95% number of deletions = 4,468,046 mapped reads with deletion percentage = 1.12% homopolymer indels = 40.55% >>>>>>> Coverage mean coverageData = 12.1845X std coverageData = 150.6354X There is a 91.33% of reference with a coverageData >= 1X There is a 90.57% of reference with a coverageData >= 2X There is a 89.17% of reference with a coverageData >= 3X There is a 87.06% of reference with a coverageData >= 4X There is a 84.09% of reference with a coverageData >= 5X There is a 80.29% of reference with a coverageData >= 6X There is a 75.71% of reference with a coverageData >= 7X There is a 70.49% of reference with a coverageData >= 8X There is a 64.8% of reference with a coverageData >= 9X There is a 58.83% of reference with a coverageData >= 10X There is a 52.77% of reference with a coverageData >= 11X There is a 46.8% of reference with a coverageData >= 12X There is a 41.06% of reference with a coverageData >= 13X There is a 35.66% of reference with a coverageData >= 14X There is a 30.68% of reference with a coverageData >= 15X There is a 26.16% of reference with a coverageData >= 16X There is a 22.13% of reference with a coverageData >= 17X There is a 18.58% of reference with a coverageData >= 18X There is a 15.5% of reference with a coverageData >= 19X There is a 12.86% of reference with a coverageData >= 20X There is a 10.61% of reference with a coverageData >= 21X There is a 8.73% of reference with a coverageData >= 22X There is a 7.16% of reference with a coverageData >= 23X There is a 5.86% of reference with a coverageData >= 24X There is a 4.79% of reference with a coverageData >= 25X There is a 3.92% of reference with a coverageData >= 26X There is a 3.2% of reference with a coverageData >= 27X There is a 2.63% of reference with a coverageData >= 28X There is a 2.16% of reference with a coverageData >= 29X There is a 1.78% of reference with a coverageData >= 30X There is a 1.47% of reference with a coverageData >= 31X There is a 1.23% of reference with a coverageData >= 32X There is a 1.03% of reference with a coverageData >= 33X There is a 0.87% of reference with a coverageData >= 34X There is a 0.74% of reference with a coverageData >= 35X There is a 0.63% of reference with a coverageData >= 36X There is a 0.55% of reference with a coverageData >= 37X There is a 0.48% of reference with a coverageData >= 38X There is a 0.42% of reference with a coverageData >= 39X There is a 0.38% of reference with a coverageData >= 40X There is a 0.34% of reference with a coverageData >= 41X There is a 0.31% of reference with a coverageData >= 42X There is a 0.28% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.22% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.19% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3487265992 13.991002221013524 383.4696022034587 chr2 243199373 3187971713 13.108470115175832 89.27195935686069 chr3 198022430 2556128460 12.908277410796343 33.240534666016906 chr4 191154276 2257349830 11.809047002432736 101.06026688651826 chr5 180915260 1813617403 10.024678974012474 14.945326129088736 chr6 171115067 1853035905 10.829180255646337 46.622628040293584 chr7 159138663 2131548176 13.39428229329789 95.24159967326109 chr8 146364022 1939887047 13.253851735503687 131.56382014026136 chr9 141213431 1793966735 12.70393844477867 116.26910321588188 chr10 135534747 1871888070 13.811130440225782 333.27591751174646 chr11 135006516 1710627802 12.670705479134059 64.19721035982056 chr12 133851895 1415806279 10.577409300032697 15.836006867534818 chr13 115169878 1154519998 10.024496144729788 7.393865635420341 chr14 107349540 828816520 7.7207272616165845 12.376069887994772 chr15 102531392 995216913 9.706460563804693 7.499795813309418 chr16 90354753 1403835659 15.536932063773115 157.01688690561335 chr17 81195210 803465467 9.895478649541026 38.04742619078378 chr18 78077248 1435165898 18.381358651370498 146.19933916576673 chr19 59128983 833430557 14.095127545149897 187.50727541816636 chr20 63025520 734917738 11.66063743702551 36.607753476943955 chr21 48129895 528633649 10.98347812726373 56.07547157994907 chr22 51304566 433920630 8.457739024631843 9.914029718379751 chrMT 16571 8536914 515.1719268601775 93.2387649822775 chrX 155270560 2410112231 15.522016736463113 49.35443334599659 chrY 59373566 129835920 2.1867630453592763 114.31832561056095