The line segments missing from the graph indicate that there are no individuals with the double-recombinant (AA,BB) and (BB,AA) genotypes.
But I would expect that the output would have NA for those values, such as in the example below, where the (AA,BB) genotype is absent.
karl
set.seed(20210729)
library(qtl)
data(fake.f2)
fake.f2 <- sim.geno(fake.f2, n.draws=128, step=1)
(out_effplot <- effectplot(fake.f2, mname1="1@5", mname2="1@7"))
$Means
1...@7.0.AA 1...@7.0.AB 1...@7.0.BB
1...@5.0.AA 21.44141 20.17869 NA
1...@5.0.AB 22.67253 24.56918 18.60580
1...@5.0.BB 17.75186 22.19160 25.44724
$SEs
1...@7.0.AA 1...@7.0.AB 1...@7.0.BB
1...@5.0.AA 0.6455828 4.4105666 NA
1...@5.0.AB 5.4346461 0.5265628 9.3071026
1...@5.0.BB 4.5490475 6.8012948 0.7549752