A recent Science paper by Li et al. (2016) provides really cool results for the fitness of SNPs at a single gene in yeast. By combining precise gene replacement and next-generation sequencing, the authors quantified fitness for more than 65k different yeast strains, each carrying a unique variant of the single-copy tRNA-Arg-CCU gene. They conclude that approximately 1% of the mutations were beneficial, whereas 42% were deleterious. Many mutation pairs exhibited strong negtive epistasis.
A figure from Li et al. showing the fitness of strains with 1, 2 and 3 mutations, respectivey. A value <1 at the x-axis implies that the mutated strain had lower fitness than the wild type.