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This application benefits from high diversity, because overlapping individual reads are likely to share informative SNPs, and errors can be more clearly identified because of high coverage.
Genes from independent loci, which share informative words, receive a high GRAIL similarity score and are more likely to be functionally related.
Additive and shared informative variation was crucial for inferring reticulation patterns or added to the phylogenetic information content of the data (see below).
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In the other sequence, there were also 3 regions of similarity, 142, 4, and 42 nucleotides in length, containing 45, 0, and 3 shared informative sites.
The small sample size in our cohort may explain our inability to detect a difference in shared informative sites between these 2 groups.
In the other, there were 3 regions of similarity, 8, 42, and 3 nucleotides in length, containing 1, 32, and 3 shared informative sites.
In one of these, there were 3 regions, 132, 4, and 44 nucleotides in length, containing 43, 2, and 5 shared informative sites, for which the closest matching sequence was from his partner F10.
In one sequence, there were 2 regions of similarity, 27 and 13 nucleotides in length, containing 15 and 7 shared informative sites that were detected by the InSites algorithm.
While RIP 3.0 found 2 sequences in one individual that may have recombined with his partner's virus at a 90% confidence level, we were unable to detect a difference in the number of shared informative sites that InSites revealed in the enrolled couples versus the pairs with no known epidemiologic link.
