Physiotherapy in patients after injury to soft parts of the knee joint

Genotype calls for all individuals at first codon positions

Genotypes All Sites Part 3 of 4

Genotype calls for all individuals at all sites. Part 3 of 4

Genotypes All Sites Part 4 of 4

Genotype calls for all individuals at all sites. Part 4 of 4

Genotypes All Sites Part 1 of 4

Genotype calls for all individuals at all sites. Part 1 of 4

Genotypes All Sites Part 2 of 4

Genotype calls for all individuals at all sites. Part 2 of 4

Analyses of chromosomes 11 and 12

[2 files] Statistics calculated in 50kb sliding windows for chromosomes 11 and 12. Nucleotide diversity, absolute divergence and Kst

multiple_regression_v2

[14 files] Data and R code used for multiple regression analysis of neutral diversity. The raw unprocessed data are given in the files "set80.Zupdated.realign80.GQ30.4D.lowCUB.autoScafs.PiDxyGC.w100m150s100.csv" (pi, dxy and gc content for 100 kb windows); "set80.Zupdated.realign80.GQ30.4D.autoScafs.PiDxyGC.w100m250s100.csv" (the same but only for low-CUB genes); "mel1_hec1_wal1_hecu1_era1.realign80.GQ30.ALLSITES.cons.codeml_nW.w100m500.csv" (Paml analysis results, where branch 8..1 refers to the branch leading to H. melpomene); and "MK_gene_a.csv" (gene by gene a estimates). The "model data" files give the processed data that is imported by the R scripts to run the model, as described in the text

diversity_around_substitutions.tar

[5 files]. Nucleotide diversity (pi) and divergece (dx) for each 4D site. The "distToNearest" files give, for each 4D site, the distance to the nearest substitution, either synonymous or nonsynonymous. For synonymous substitutions, the there are 100 bootstrapped distances, obtained by subsampling sysnonymous substitutions. There are distance files for two groups of substitutions, identified using different outgroups, as described in the text

Nucleotide diversity for 100 kb windows V2

[17 files] Nucleotide diversity for each population calculated in 100kb windows. Seven different types of sites were considered: all sites, intergenic, intron, codon positions 1, 2 and 3, and four-fold degenerate (4D) sites. Dxy values between populations are also given, but these are based on just a single pair of samples and may be less accurate than those given in the dxy data. There are 8 files giving nucleotide diversity statistics considering only samples with at least 25x coverage - which should be more reliable. These correspond to the same seven site types listed above, plus one file for 4D sites only in genes showing minimal codon usage bias (CUB). There are also two files giving nucleotide diversity at intergenic sites and 3rd codon positions that were used to test whether the proportion of missing data in H. melpomene samples was correlated with nucleotide diversity

Alpha

Estimates of alpha, the genome-wide proportion of adaptive substitutions, at different minor allele frequency thresholds