BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961015.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 = 409,951,378 number of mapped reads = 394,753,162 (96.29%) number of supplementary alignments = 6,803,862 (1.66%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,747,693 number of mapped paired reads (second in pair) = 192,005,469 number of mapped paired reads (both in pair) = 383,057,660 number of mapped paired reads (singletons) = 11,695,502 number of mapped bases = 38,688,528,040 bp number of sequenced bases = 38,677,163,764 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,738,063 duplication rate = 11.65% >>>>>>> Insert size mean insert size = 87,858.2647 std insert size = 2,854,165.7844 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.151 >>>>>>> ACTG content number of A's = 11,304,395,001 bp (29.23%) number of C's = 7,999,961,250 bp (20.68%) number of T's = 11,248,392,591 bp (29.08%) number of G's = 8,048,307,853 bp (20.81%) number of N's = 76,107,069 bp (0.2%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 399,711,726 number of insertions = 3,946,846 mapped reads with insertion percentage = 0.97% number of deletions = 4,646,948 mapped reads with deletion percentage = 1.14% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 12.4975X std coverageData = 155.9641X There is a 91.36% of reference with a coverageData >= 1X There is a 90.65% of reference with a coverageData >= 2X There is a 89.36% of reference with a coverageData >= 3X There is a 87.39% of reference with a coverageData >= 4X There is a 84.61% of reference with a coverageData >= 5X There is a 81.02% of reference with a coverageData >= 6X There is a 76.67% of reference with a coverageData >= 7X There is a 71.67% of reference with a coverageData >= 8X There is a 66.18% of reference with a coverageData >= 9X There is a 60.38% of reference with a coverageData >= 10X There is a 54.45% of reference with a coverageData >= 11X There is a 48.55% of reference with a coverageData >= 12X There is a 42.84% of reference with a coverageData >= 13X There is a 37.42% of reference with a coverageData >= 14X There is a 32.37% of reference with a coverageData >= 15X There is a 27.77% of reference with a coverageData >= 16X There is a 23.63% of reference with a coverageData >= 17X There is a 19.96% of reference with a coverageData >= 18X There is a 16.75% of reference with a coverageData >= 19X There is a 13.97% of reference with a coverageData >= 20X There is a 11.6% of reference with a coverageData >= 21X There is a 9.59% of reference with a coverageData >= 22X There is a 7.9% of reference with a coverageData >= 23X There is a 6.49% of reference with a coverageData >= 24X There is a 5.33% of reference with a coverageData >= 25X There is a 4.37% of reference with a coverageData >= 26X There is a 3.59% of reference with a coverageData >= 27X There is a 2.95% of reference with a coverageData >= 28X There is a 2.43% of reference with a coverageData >= 29X There is a 2.01% of reference with a coverageData >= 30X There is a 1.66% of reference with a coverageData >= 31X There is a 1.38% of reference with a coverageData >= 32X There is a 1.16% of reference with a coverageData >= 33X There is a 0.98% of reference with a coverageData >= 34X There is a 0.83% of reference with a coverageData >= 35X There is a 0.71% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.53% of reference with a coverageData >= 38X There is a 0.47% of reference with a coverageData >= 39X There is a 0.42% of reference with a coverageData >= 40X There is a 0.37% of reference with a coverageData >= 41X There is a 0.34% of reference with a coverageData >= 42X There is a 0.31% of reference with a coverageData >= 43X There is a 0.28% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.24% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.22% of reference with a coverageData >= 48X There is a 0.21% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.19% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3576360879 14.3484532341446 395.4136029910138 chr2 243199373 3268950787 13.44144413974291 92.93219067599557 chr3 198022430 2619887290 13.230255229167726 34.592620090999446 chr4 191154276 2317031091 12.121262152670862 106.65374581044168 chr5 180915260 1858842182 10.274656665225477 15.415296155649319 chr6 171115067 1899272039 11.099385181551547 48.27294880290696 chr7 159138663 2183886279 13.72316593485519 97.99296453835586 chr8 146364022 1990278492 13.598140204154817 140.06061042394413 chr9 141213431 1843193300 13.052535349842183 122.35619397764344 chr10 135534747 1921976691 14.180693390750934 345.2004136343062 chr11 135006516 1753591579 12.988940318999122 66.6659044461801 chr12 133851895 1450781790 10.838709380991581 13.310416719170519 chr13 115169878 1184210759 10.28229585343487 7.59084217699682 chr14 107349540 850034243 7.918378066640994 12.67675791357221 chr15 102531392 1021792943 9.965659522110068 7.646044090024068 chr16 90354753 1439090575 15.92711536713514 161.01582613523192 chr17 81195210 824516154 10.15473885713209 39.58393253046178 chr18 78077248 1473695909 18.874844423307543 151.78870759997685 chr19 59128983 855057009 14.460877992777247 193.83954425940058 chr20 63025520 754089890 11.964834086255854 38.43724710560783 chr21 48129895 542686419 11.27545403953198 57.1627271702665 chr22 51304566 444794058 8.669677821658212 10.247123992964045 chrMT 16571 8743511 527.6393096373182 94.1103734432249 chrX 155270560 2470923891 15.913666383376217 51.07277915233033 chrY 59373566 134840280 2.2710490388938402 121.97798958784243