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In contrast to those studies, the mutation frequencies obtained from our MMR deletion mutants showed that the bacterial-like MMR pathway encoded in the genome of H. salinarum NRC-1 is not essential for maintaining the low genomic mutation rate we observed in this organism.

Table 2 shows the mutation frequencies obtained here and from the COSMIC (Catalog of Somatic Mutations in Cancer) database [ 21].

In fact, mutation frequencies obtained with various concentrations of the tested samples do not change significantly when compared to spontaneous mutation frequencies.

Furthermore, we suggest that such studies should use an average mutation frequency of 5 × 10−4 given the relatively stable mutation frequencies obtained in this study.

Using low fidelity CVB3 variants that generate subtle, yet biologically confirmed, differences in mutant composition, we showed that detected variation frequencies correlated with the mutation frequencies obtained by molecular cloning in the original paper (Gnädig et al., 2012).

We analyze the population structure using microsatellite markers, revisit their colonization history into the island using mtDNA sequences and estimate their age since the first colonization event based on the calculation of mutation frequencies obtained from whole mtDNA sequences.

Similar(54)

Thus, the low mutation frequency obtained in the present study is not due to the methods used.

Within the group of TNBC patients, a higher mutation frequency was obtained (23.3 %; 7/30) than in the group of patients diagnosed before the age of 50 (7.7 %; 6/78).

Pair-wise analysis showed that for strains of 9a5c, Ann1 and Dixon, the lowest mutation frequency was obtained when each of them was compared with Temecula-1, which indicates a closer phylogeny relationship of these strains to Temecula-1.

It was unfortunately not possible to pool our data with nucleotide mutation frequency data obtained in various other published evolution experiments, where either input virus sequences were unknown and mutation counts were inferred by maximum likelihood or parsimony based approaches [ 17, 18, 28], or where observed mutations were derived only from small portions of the virus genome [ 66].

When Pfu polymerase was used instead of Taq comparable results (mixed sequences, a Gp C context bias, mutation frequencies ∼13 kb−1) were obtained including the same Gp C bias (Supplementary Figure S2).

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