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Luo et al. produced an n = 2 strain containing chromosomes that were each about 6,000 kb long.

Subsequently, adjacent bins with the same genotype within a physical distance of 100 kb were merged into larger bins to remove bins with spurious or missing genotypes.

A minimum of three RGAs of the same class that were less than 300 kb apart were arbitrarily considered forming a multi-gene locus.

Features were calculated among rare SNVs within 10 kb of the gene.

For one sample, a 5 kb library was discarded as it was error prone and could not be processed by the Allpaths-LG PrepareAllPathsInputs.pl script.