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Of the remaining reads, if a read could be mapped only to one genome, the allelic origin is obvious, while if a read could be mapped to both genomes with different edit distances, the strain with smaller edit distance was assigned as the allelic origin.
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The next closest genome pair with different cps loci was NCSR101 and ATCC BAA-2146 (both ST11), which differed by 500 SNPs across the rest of the genome, whereas all other pairs of genomes with different cps loci differed by >1,000 SNPs.
Genomes with different cps loci also differed substantially in terms of gene content outside the cps locus (mean 809 genes different between pairs of genomes).
Using a single virtual viral community, composed of 300 genomes with different degrees of relatedness, from both ssDNA (Microviridae, Circoviridae, and Nanoviridae) and dsDNA (Siphoviridae, Podoviridae, and Myoviridae) viral families, we generated a large number of metagenomic reads mimicking Roche's 454 and Illumina's GAIIx sequencing platforms.
Alternatively, given the mounting evidence for recombination in plant mtDNA [ 41, 46, 54] and the existence of rate variation both within and among species [ 7], rate discrepancies between genes may be the result of recombination between genomes with different mutational histories.
progressiveMauve excels at aligning rearranged genomes with different gene content.
In a separate experiment, we applied smyRNA to a set of genomes with different types.
For instance, two individuals with identical genetic makeup may have distinct set point viral loads because viral genomes with different fitness may get fixed in the two patients by sheer chance.
There are many AMs used to annotate prokaryotic genomes with different tools being developed.
We annotated TE sequences from 10 fungal genomes with different TE content (1-70%).
The surviving fractions for genomes with different numbers of mutations are calculated as follows.
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CEO of Professional Science Editing for Scientists @ prosciediting.com