BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777247.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 18,033,628 number of mapped reads = 17,935,216 (99.45%) number of supplementary alignments = 461,367 (2.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,968,680 number of mapped paired reads (second in pair) = 8,966,536 number of mapped paired reads (both in pair) = 17,906,556 number of mapped paired reads (singletons) = 28,660 number of mapped bases = 1,630,461,815 bp number of sequenced bases = 1,629,877,919 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,062,060 duplication rate = 35.76% >>>>>>> Insert size mean insert size = 295,520.5738 std insert size = 5,386,547.0119 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 54.2508 >>>>>>> ACTG content number of A's = 416,644,695 bp (25.56%) number of C's = 342,798,889 bp (21.03%) number of T's = 473,658,501 bp (29.06%) number of G's = 396,718,275 bp (24.34%) number of N's = 57,559 bp (0%) GC percentage = 45.37% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 7,039,995 number of insertions = 95,119 mapped reads with insertion percentage = 0.52% number of deletions = 331,060 mapped reads with deletion percentage = 1.82% homopolymer indels = 50.05% >>>>>>> Coverage mean coverageData = 0.5267X std coverageData = 8.6656X There is a 6.85% of reference with a coverageData >= 1X There is a 3.4% of reference with a coverageData >= 2X There is a 1.95% of reference with a coverageData >= 3X There is a 1.44% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.98% of reference with a coverageData >= 6X There is a 0.87% of reference with a coverageData >= 7X There is a 0.8% of reference with a coverageData >= 8X There is a 0.74% of reference with a coverageData >= 9X There is a 0.7% of reference with a coverageData >= 10X There is a 0.66% of reference with a coverageData >= 11X There is a 0.63% of reference with a coverageData >= 12X There is a 0.6% of reference with a coverageData >= 13X There is a 0.58% of reference with a coverageData >= 14X There is a 0.56% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.5% of reference with a coverageData >= 18X There is a 0.49% of reference with a coverageData >= 19X There is a 0.47% of reference with a coverageData >= 20X There is a 0.46% of reference with a coverageData >= 21X There is a 0.44% of reference with a coverageData >= 22X There is a 0.43% of reference with a coverageData >= 23X There is a 0.42% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.4% of reference with a coverageData >= 26X There is a 0.39% of reference with a coverageData >= 27X There is a 0.38% of reference with a coverageData >= 28X There is a 0.37% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.35% of reference with a coverageData >= 31X There is a 0.34% of reference with a coverageData >= 32X There is a 0.33% of reference with a coverageData >= 33X There is a 0.33% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.31% of reference with a coverageData >= 36X There is a 0.31% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.29% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.28% of reference with a coverageData >= 41X There is a 0.27% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.26% of reference with a coverageData >= 44X There is a 0.26% of reference with a coverageData >= 45X There is a 0.25% of reference with a coverageData >= 46X There is a 0.25% of reference with a coverageData >= 47X There is a 0.24% of reference with a coverageData >= 48X There is a 0.24% of reference with a coverageData >= 49X There is a 0.23% of reference with a coverageData >= 50X There is a 0.23% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 161106163 0.6463621328349669 10.160969854395226 chr2 243199373 145661070 0.598936864857789 8.963108605344102 chr3 198022430 93398503 0.47165618056499964 7.767352271610711 chr4 191154276 78316695 0.4097041229671472 7.369016974983078 chr5 180915260 86091331 0.4758655018929857 7.543293823147947 chr6 171115067 75065534 0.4386845373470239 7.720630781103529 chr7 159138663 111704168 0.7019297881118933 11.090499831366207 chr8 146364022 54513721 0.37245301307721645 7.298867860369782 chr9 141213431 57759788 0.40902474779470516 6.78302110528697 chr10 135534747 72701092 0.5364018719125953 8.44430038665179 chr11 135006516 105854279 0.7840679260251409 11.221505303060265 chr12 133851895 90512157 0.6762112482606242 9.350002953328316 chr13 115169878 51814895 0.44989971249253213 8.167527025216893 chr14 107349540 37264128 0.34712890246199474 6.580580308789502 chr15 102531392 74138319 0.7230792204596227 9.869438571527464 chr16 90354753 51354769 0.5683682074810166 7.469154315479273 chr17 81195210 68683352 0.8459039886712529 10.395775782114049 chr18 78077248 27474208 0.35188494348571303 7.634890375385961 chr19 59128983 59484086 1.0060055658322418 13.406468444913747 chr20 63025520 48859200 0.7752288279414434 13.598763579548182 chr21 48129895 11448056 0.23785748961222541 5.029538784287331 chr22 51304566 21226027 0.4137258855283953 6.552115473659479 chrMT 16571 342737 20.68294007603645 12.910518191277033 chrX 155270560 44888648 0.28909954340346294 6.003844474263016 chrY 59373566 798889 0.013455297598261152 0.8532012960533841