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In addition, Simoncelli et al. also proposed the concept of joint shiftability, which allows shiftability in the subset of position, orientation, and scale to be achieved simultaneously.
First, the position data (gray) is implicitly assumed to be locally linear, such that a straight line can be fitted to the subset of position data within a moving window.
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A statistically significant (0.001≤p≤0.008) concentration of mutations occurs in a subset of positions (set AAT TAT) that is conserved (≥75% identical) in AATases and variable (<75% identical) in TATases.
This latter subset of positions was further assayed for the presence of potential mutations.
Therefore, where G i is the subset of positions of the base pairs belonging to the gene i and.
Let K denote the subset of positions of the base pairs belonging to the genes used for silent mutation detection and let L denote the subset of positions of the base pairs belonging to the genes which have at most one non-silent mutation across all samples.
Furthermore, we assume the sequence label to be directly affected by only a small subset of positions in the copy number profile.
A N-map of s over t is nothing but a peculiar type of map from a subset of positions of s to the set of positions of t.
The bases called in the pileup files were compared to the YO516, YO528 SNP table and converted into parent 1 (Yor96) or parent 2 (YO795) allele calls for the subset of positions polymorphic between the parents.
Using Cake and an intersection of any two or more callers, we made 1225 calls (per sample 613 ± 42), of which 254 were from a reference call set representing a subset of positions (264) covered by the capture baits where a somatic mutation had resulted in a non-synonymous change; a sensitivity of 96.2% (Table 1, Supplementary Fig. S4).
In comparison with base calls that represent variant alleles, base calls that represent sequencing errors are more likely to cluster on one strand of the DNA (sequencing error rates on the forward and reverse strands are likely independent), cluster in a subset of positions in reads (toward the 3′-end of the read for Illumina reads) and have lower base-quality values.
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