The diversity panel analysis was carried out with the following filters on three replicates of 54 accessions including Salinas and Seriola (RIL population parents). The parents can be distinguished by their name SAL or SEL in the diversity panel. SAL_A or SAL_B correspond to two separate sets of CEL files, generated from three replicates each. Similarly SER_A and SER_B.
Fixed Filter Settings for Analysis
- Maximum frequency of major allele (A,B,C,D or -) = 95% (at least one rare allele in the entire panel)
- Maximum percentage of inconsistent genotype calls among 3 replications of each accession/line (haplotypes were called “I” when calls were AAB, BBA or AB- ) = 40%
- Maximum percentage of missing data (where all three chip replications returned missing value) = 95%
- Minimum number of valid probe at each position = 2%