Nucleotide composition was highly A/T skewed, with mean base pair frequencies for NAD1 and NAD4 of A: 0.46, C: 0.12, G: 0.09, T: 0.33 and A: 0.43, C: 0.15, G: 0.08, T: 0.33, respectively.
Specifically, we used estimates of marginal probabilities of base pairs obtained from base pair frequencies from the Gibbs sampler after a burn-in period to obtain the γ-centroid estimators.
This is the result of the fact that in general the G C→A T base pair transition frequency is significantly higher than that of the reverse T A→C G transition.
An initial 32.0-Mbp screen of genomic DNA and cDNA templates in the CMMB resulted in the identification of 22 point mutations, with a per-base-pair mutation frequency of 1 in 1.454 Mbp (Table 1).
Even at 1 mutation per exon, which is lower than observed, the resulting frequency of 0.009 changes per base pair differs from the frequency of synonymous changes by an order of magnitude.
The average SNP frequency was 1.08 × 10-2 per base pair of DNA and the average INDEL frequency was 2.06 × 10-2 per base pair of DNA.
Finally, the frequency of base pair differences between pairs of actinomycete strains (relative genetic distance) was determined in PAUP* 4.0b 10 [61] and inserted as a continuous covariate in the statistical analyses (Tables 2 and 3; see below).
The target variables could be, for instance, pleiotropic additive effects of many loci under the infinitesimal model of Fisher (1918), correlated allelic frequencies of loci within bins of physical distance defined by numbers of base pairs, or sets of allelic frequencies that vary at random over clusters of individuals or sub-populations.
The frequency of base pair substitutions was 0.8-1.0 0.8-1.0
The observation that triplet codons appear scaled precisely to the same repeat frequency of base pairs defining the width of the minor groove, and therefore defining the intrinsic flexibility of DNA, is probably no happy accident.
