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Bulk of RMA DNA was used as a reference against which mutations were assigned.
Dystrophin mutations were assigned to mRNA isoforms as follows (Figure 1).
Mutations were assigned to isoform Dp427m ('A') if their PTCs were located 5' of the first base of the ATG of the Dp260 isoform at c.4072-296.
In the mutation step, random point mutations were assigned to individual organisms according to a Poisson distribution such that, on average, each organism received one point mutation per generation.
Mutations were assigned to a given chromosome through homozygous rec12Δ crosses.
High-clonality LOH mutations were assigned a value of 1, low-clonality mutations were assigned a value of 0.5, and MSI 0.75 at the first loci, and 0.5 for additional loci.
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Then random mutations are assigned to each by the spin of a "wheel of fortune", while changes in the environment are represented by the changing height of the canopy.
Of note, the AAT mutations are assigned letter names based on the electro-phoretic mobility of the protein product, which is in turn determined by its isoelectric point.
Additional comparison of the methods has been conducted using the BS292 set (Table 5), where all mutations are assigned by UniProt as benign.
Indels and mutations are assigned scores based on the frequency of their occurrence over time (Dayhoff, 1978; Henikoff and Henikoff, 1992).
The currently proposed seven levels of confidence scores (viable: V1 V4, non-viable: N5 N7) that are assigned to predictions and assessment of possible sequence changes are as follows: (V1) VIABLE Highest confidence for viable mutations is assigned based on codons observed in the reference library (eg, DENV-2 codon frequency matrix; Observation O0).
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