Fig. 3

Effect of sequencing parameters on the accuracy and precision of the measurement. Simulated reads were generated for each domain and aligned back to the genome. RMSE was calculated at the domain level (do reads align to the exact genomic location from where they originated?), at the gene-specific clade level (do reads align to the correct clade within the originating NBPF gene?), at the group-specific clade level (to the correct clade within gene groupings described above), and at the clade-specific level (do reads align to the correct clade?)