I have a data of 283 F2 fish. These were obtained from a single pair of F1 parent and F0 grand parent. The F0 was obtained from natural population (mother from marine and father from pond) and the genotypes are not homogeneous and some are unknown (e.g., A- and BC; "-"= unknown). Alleles are differing with the loci (e.g., allele of the some of the locus is A and B, for some is A, B and C and some contains A, B, C and D.
What should I call for analyzing my data in R/qtl? inbreed or out breed? Please help me to define my data set.