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Our analysis of self-diagnosis apps suggests that they inhabit a contested and ambiguous site of meaning and practice.
At the other thirteen sites, one strain genotype was reported only as "N" (ambiguous site).
Nuclear gene sequences containing more than one ambiguous site were resolved using PHASE version 2.1.1 [ 36], for which the input files were prepared using SeqPHASE [ 37].
The remaining spectral redundancy came exclusively from ambiguous site localizations, where there was sufficient evidence to identify both peptides, but the position of the modified amino acid remained ambiguous.
In addition, LT-PCR amplification and sequencing with multiple internal primers verified an ambiguous site in CR1 of red-footed booby individual rf_CocD7, and re-sequencing of a subset of individuals with ambiguities verified our original results.
In the case of sites with ambiguity (e.g., T/A) in the PAG2014 data, if one of the two possible alleles matched an allele present in the 1000G, we considered this an allele match and PAG2014 was corrected, by attributing the allele present in the 1000G data to the ambiguous site.
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We suggest that this observation resulted from ambiguous site-level responses to salvage that collectively contributed to the (mostly negative) significant responses at the landscape level.
Wang, which was not included in Xu et al. (2012a) because of the presence of an access of ambiguous sites in its ITS sequence in the GenBank (i.e., FJ501349), were added in current analyses to test for its putative relationships with the new species.
Sequences that contained unusual base substitution rates or large amounts of ambiguous sites were also discarded.
All ambiguous sites of the alignments were removed from the dataset for phylogenetic analyses.
We used 401-bp COI and 423-bp ND4 sequences, excluding ambiguous sites.
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