For each dish, a maximum of 100 clones were sequenced, till the isolate with mutant allele was identified.
HVS-I (minimum length sequenced was nucleotide positions (np) 16080-16569; maximum length sequenced np 16001-16569) and HVS-II (minimum length sequenced np 1-207; maximum length sequenced np 1-575) were sequenced in all samples as described elsewhere [ 47].
As the method allows input of different sample sizes per locus, the maximum number of individuals that were sequenced for each locus was used.
Maximum DNA parsimony analyses were conducted using sequence from exons that were sequenced in all strains of mice using the DNAPars program included in the Phylogeny Interference Package (Phylip) version 3.66 [ 30].
From the 12 amplicons that were selected for sequencing and cloning, a maximum length of approximately 7,773 bp was sequenced per genotype.
We obtained an average coverage depth of 3.9 (number of times each nucleotide was sequenced), with a maximum depth of 429 (25% percentile = 1; 75% percentile = 5).
Another reason for a redundant maximum score sum is sequence identity around SV breakpoints (Supplementary Fig. S2).
These theoretical maxima are conservative as all sequences may not be as long as the longest sequence, and all possible matches for all sequence lengths may not be found.
For Mafft, as both sequence lengths are included in the additional scaling factor, the theoretical maximum is the longest sequence length times the square of the number of different sequence lengths.
Many nonmodel plants such as Flaveria [ 4], Leymus chinensis [ 5], and Panicum maximum [ 6] have been successfully sequenced at the transcriptome level, and some common underlying evolutionary mechanisms have been elucidated through comparative analyses of related species [ 4, 7, 8].
