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This result suggests that the space environment preferentially induced mutations at polymorphic sites in rice genomes and might share a common mechanism with other types of mutagens.
However, the detection of structurally disrupting mutations at polymorphic proportions (Table 1) predicts that MT4 is inactive in some individuals.
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Nonpolymorphic mutations occurring at polymorphic positions, defined as positions with mutations occurring at >1% in any subtype, were generally excluded.
If we adopt this rationale then we will always discard those legitimate somatic mutations that occur at polymorphic sites (it is ironic too that polymorphic sites are actually markers of mutation events sometime in the past).
ClonalFrame estimates the probability of recombination versus mutation at each polymorphic site in the alignment.
Private polymorphisms are defined as polymorphic mutations at a specific site that occur only in 1 of the 2 species.
We suspected such a deleterious effect of polymorphic mutations at the EF1α locus in Bathymodiolus [26].
Ten mutations were not added because they occur at polymorphic positions (L10F/R, K20T, K43T, V71I/L, T74P, L89V/T, and I93M).
Although they occur at polymorphic positions, we included the protease mutations V82A/T/F/S/C/M/L because of their substantial contribution to resistance to several PIs.
Two mutations (E44A and T69N) were not added because they occur at polymorphic positions.
Regardless of the list that is used to define mutations associated with transmitted resistance, the occurrence of polymorphic resistance-related mutations at low levels among some sequences studied is highly probable.
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