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A filtered set of 29,464 high quality SNPs (maximum heterozygosity 10%, maximum missing data 66%) were identified.
Using a maximum missing data (MMD) threshold of 25% in the RIL population for each locus, a total of 1,765 SNP loci were finally recovered.
The SNPs were filtered out from the GBS pipeline output using a threshold of 5% minimum allele frequency and 20% maximum missing data.
Of the 337 completed, the maximum missing data for any scenario response on completed questionnaires was less than 2% (n<7).
After removal of failed SNPs and samples, the genotype calling rate was 99.93%, with maximum missing data rate per sample of 2.1% and maximum missing per SNP of 4.98%.
To maximize the information content of our sequences and minimize the impact of missing data, the 559 single-copy orthologous groups were further filtered with stricter constraints on length (minimum 200 amino acids) and sequence alignment (maximum missing data 50% in the CDS alignments), and the resultant 276 groups were used for phylogenetic tree reconstruction.
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The maximum percent missing data allowed was 20%.
In each of the versions: NA20, NA50, and NA70, missing values were introduced at random but the maximum percent missing data at a given marker was set to 20%, 50%, and 70% respectively.
For any given variable, the maximum amount of missing data was less than 5%.
The maximum proportion of missing data for a single variable was 72%.
Imputation parameters in Maskov were set to E = 5 with the default threshold of E, and the maximum amount of missing data set at seventy percent.
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