All samples were run in duplicate and were repeated if profiles did not replicate according to Rotor-Gene analysis software (version 5).
Bootstrap confidence values were calculated on 1,000 replicates according to the maximum likelihood approach of Felsenstein (20 ).
The samples listed in Table 1 were sequenced as multiple technical replicates according to the schematics shown in Figures 1 and 2. The samples were chosen to include a trio (NA12878-NA12891-NA12892) with numereferencerencallsetsets both public and internal, ethnic diversity (NA18507) and a sample (NA10080) with a known disease mutation and internal reference materials.
Parameter estimates and standard errors were combined across the five replicates according to the procedure described by Rubin [ 16] and Carlin et al. [ 17] (procedure 'micombine' in STATA).
Ten days after sowing, assessment of disease severity was carried out in 20 replicates according to the following disease index scale: 1 = no visible symptoms, 2 = mild symptoms on roots, 3 = severe symptoms on roots and wilting, 4 = dead plants.
These findings are replicated across Wales, according to recent surveys, which showed less than 1% of the population have a fully healthy lifestyle, with 5% not following any of the five recommended points.
For fatty acid profiling analysis, total lipids were extracted from three independent biological replicates according to the method of Lepage and Roy [ 43], with modifications.
Random rearrangement operations on the initial genomes were performed for the number of replicates according to the number of rearrangements inferred by GRAPPA.
Zeleny sedimentation values were measured for each line with three replicates according to Axford et al. [74].
The relative quantification of the genes of interest was performed in triplicate using three biological replicates according to the comparative method.
