Library Enrichment Calculations
The fasta files containing the annotated R genes for each Illumina
library were concatenated into a fasta containing every observed R gene
from the Illumina dataset (hence, a “Pan-NLRome”). Reads from each
Illumina RenSeq library, as well as eleven 1X-depth WGS libraries from
seven S. integrifolium , two S. perfoliatum , one S.
laciniatum and one S. terebinthinaceum , were mapped to the
Pan-NLRome using bwa mem (Li 2013). The fraction out of the total
reads in the library that mapped to the Pan-NLRome with a SAM CIGAR
mapping score of between 148M-151M was calculated, representing reads
that mapped to an R gene in the Pan-NLRome with between 98.01%-100%
identity.