BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618654.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 52,129,613 number of mapped reads = 50,552,426 (96.97%) number of supplementary alignments = 160,586 (0.31%) number of secondary alignments = 0 number of mapped bases = 4,888,595,477 bp number of sequenced bases = 4,884,911,560 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,355,041 duplication rate = 51.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.7897 >>>>>>> ACTG content number of A's = 1,327,929,700 bp (27.18%) number of C's = 1,096,238,611 bp (22.44%) number of T's = 1,438,126,797 bp (29.44%) number of G's = 1,021,901,028 bp (20.92%) number of N's = 715,424 bp (0.01%) GC percentage = 43.36% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 42,208,142 number of insertions = 927,154 mapped reads with insertion percentage = 1.8% number of deletions = 2,483,587 mapped reads with deletion percentage = 4.79% homopolymer indels = 52.13% >>>>>>> Coverage mean coverageData = 1.5792X std coverageData = 29.5845X There is a 13.48% of reference with a coverageData >= 1X There is a 9.69% of reference with a coverageData >= 2X There is a 7.75% of reference with a coverageData >= 3X There is a 6.5% of reference with a coverageData >= 4X There is a 5.61% of reference with a coverageData >= 5X There is a 4.94% of reference with a coverageData >= 6X There is a 4.41% of reference with a coverageData >= 7X There is a 3.98% of reference with a coverageData >= 8X There is a 3.62% of reference with a coverageData >= 9X There is a 3.32% of reference with a coverageData >= 10X There is a 3.06% of reference with a coverageData >= 11X There is a 2.84% of reference with a coverageData >= 12X There is a 2.65% of reference with a coverageData >= 13X There is a 2.48% of reference with a coverageData >= 14X There is a 2.33% of reference with a coverageData >= 15X There is a 2.19% of reference with a coverageData >= 16X There is a 2.07% of reference with a coverageData >= 17X There is a 1.96% of reference with a coverageData >= 18X There is a 1.86% of reference with a coverageData >= 19X There is a 1.77% of reference with a coverageData >= 20X There is a 1.68% of reference with a coverageData >= 21X There is a 1.6% of reference with a coverageData >= 22X There is a 1.52% of reference with a coverageData >= 23X There is a 1.45% of reference with a coverageData >= 24X There is a 1.38% of reference with a coverageData >= 25X There is a 1.31% of reference with a coverageData >= 26X There is a 1.24% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.12% of reference with a coverageData >= 29X There is a 1.06% of reference with a coverageData >= 30X There is a 1% of reference with a coverageData >= 31X There is a 0.95% of reference with a coverageData >= 32X There is a 0.9% of reference with a coverageData >= 33X There is a 0.85% of reference with a coverageData >= 34X There is a 0.81% of reference with a coverageData >= 35X There is a 0.77% of reference with a coverageData >= 36X There is a 0.73% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.66% of reference with a coverageData >= 39X There is a 0.63% of reference with a coverageData >= 40X There is a 0.61% of reference with a coverageData >= 41X There is a 0.58% of reference with a coverageData >= 42X There is a 0.56% of reference with a coverageData >= 43X There is a 0.54% of reference with a coverageData >= 44X There is a 0.52% of reference with a coverageData >= 45X There is a 0.5% of reference with a coverageData >= 46X There is a 0.49% of reference with a coverageData >= 47X There is a 0.47% of reference with a coverageData >= 48X There is a 0.46% of reference with a coverageData >= 49X There is a 0.44% of reference with a coverageData >= 50X There is a 0.43% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 414839307 1.6643461321606898 32.1089269687687 chr2 243199373 441273562 1.8144518900548317 42.83526806168768 chr3 198022430 297769053 1.5037137611128193 22.768911174923897 chr4 191154276 254703980 1.3324524322961 23.631399359782318 chr5 180915260 289210797 1.5985981337339923 33.34246800015009 chr6 171115067 254508978 1.4873557452424688 23.331882061706477 chr7 159138663 232344223 1.4600111539205278 21.801794001055484 chr8 146364022 229546831 1.5683282535102787 23.641200857563124 chr9 141213431 221024903 1.5651832933653458 24.9198053685662 chr10 135534747 248587938 1.8341269932794428 37.122516172794334 chr11 135006516 249488076 1.8479706268399667 33.92923439053131 chr12 133851895 214548600 1.6028805569020894 35.788116416765774 chr13 115169878 133297801 1.1574015994008433 29.516975078256813 chr14 107349540 175745923 1.6371371782310384 26.980634869806146 chr15 102531392 150444786 1.4673046280304085 23.519547460777883 chr16 90354753 162660962 1.8002479847407695 38.00477965545637 chr17 81195210 135621869 1.670318593917055 23.190441064067187 chr18 78077248 116936099 1.4976974982519875 17.746740076592857 chr19 59128983 84877811 1.4354688123081705 32.84637509076259 chr20 63025520 144622917 2.294672332731249 22.760244621915987 chr21 48129895 57468189 1.1940227378430808 16.94199360283708 chr22 51304566 70610255 1.3762957277525747 22.877471096595013 chrMT 16571 10618 0.6407579506366544 4.5842177440818395 chrX 155270560 296785060 1.9114058711451805 31.743290466916864 chrY 59373566 11666939 0.19650056053564308 16.435224094792574