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This program uses haplotype clustering that changes with genetic map position and allele frequencies to calculate a probability that an individual carries the reference allele at a locus.
Because the barley genetic map has clusters of markers with the same genetic map position, the order of some markers is unknown.
There were many sets of SNPs, ranging in size from two to 34 SNPs, with identical genetic map position; these sets were ordered so as to generate maximal LD among adjacent markers.
(A ) Genetic map position of apa-2 on chromosome X.
A model with kinship accounting for population structure was used for validating the genetic map position of the markers.
Once a genetic map position is obtained by recombination analysis, we use File S1 to estimate the corresponding physical location.
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Genetic map positions (cM) were derived from deCODE (Genethon, Marshfield).
quinquefasciatus genome at VectorBase to determine if any of these loci were within supercontigs with known genetic map positions based on RFLP marker loci [8], [17].
Genetic map positions used in the linkage analysis were obtained from the Decode map.
A comparison of genetic map positions with the rice genome is shown in Figure 3.
Sixteen contigs were therefore anchored onto 15 barley genetic map positions.
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