Additional file 5.
Table of listing synonomous/nonsynonomous changes in contigs containing SNPs that differed in frequency between the two host races. For those contigs where an open reading frame could be clearly identified, we determined whether SNPs would affect the amino acid sequence of the protein product. Contig is the R. pomonella contig number followed by the TSA accession number. CG is the D. melanogaster Celera Genome number of the locus with the closest match and Annotation is the D. melanogaster locus name where known. Position denotes the nucleotide location within the contig and synonymous? denotes whether the alternative forms of the SNP specify alternative amino acids. We also define the consensus amino acid, the alternative amino acid, the consensus codon and whether the SNP site is within the local BLAST alignment of our data with the hit to the identified D. melanogaster locus.
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Schwarz et al. BMC Genomics 2009 10:633 doi:10.1186/1471-2164-10-633