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The final linkage map had a total length of 1650 cM with 2817 recombination sites.
Consequently, for closely linked markers with less than 2 cM apart, only the one with less missing data or presented in the previously published maps (anchor markers) were kept in the final linkage map (Ahfock et al. 2014).
The final linkage map is shown in Fig. 2 and 3. Twenty chromosomes had sufficient anchoring markers to create integrated LGs following the procedures outlined in Supplement S4.
These markers, combined with the male-inherited component of the 3∶1 marker genotypes, are used for constructing the final linkage map [25], [26], [36].
Furthermore, the final linkage percentage is also directly influenced by the definition of a successful match.
The final linkage map was used for QTL analysis with the diploid half-sibs.
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Sensitivity of this final linkage was 95%.
BLAST searches were used to determine putative locations for the 64-bp sequences of the 2235 GBS markers comprising our final linkage map in the Astyanax genomic and transcriptomic data sets.
A final linkage map of the Rlm2 interval was constructed after placing markers in order based on their homologous B. rapa position and integrating the Rlm2 phenotypic data.
In total, 242 SNPs were removed due to fit and stress values above the stated threshold, resulting in a final linkage map consisting of 68 individuals with 2,589 SNPs.
Double crossover events were examined, and the original scores re-checked before a final linkage group order was assigned.
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