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Alignments of the WGS scaffolds to the optical map ordered and oriented them for tiling the ALLPATHS scaffolds.
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In addition, the 158 scaffolds in the N90 index were mapped, ordered, and oriented (supplementary fig. S1, Supplementary Material online) using conserved linkage (Schaeffer et al. 2008), in situ hybridization, and additional information (González et al. 2005; Guillén and Ruiz 2012).
Here we demonstrate the utility of the POPSEQ methodology for mapping, ordering and imputing marker data from GBS.
High missing values affected the map orders and reduced the map accuracy [ 40].
MSTMap was run with the objective function COUNT to estimate map order and Kosambi mapping function to assign genetic distances.
A genetic map was produced for each mapping population using JoinMap software to estimate linkage, map order, and distance.
A third factor likely contributing to discrepancies in map order and lengths is genotyping error (Hackett and Broadfoot 2003).
The map orders and genetic distances were determined using the build option in the CRIMAP software version 2.4 [ 7].
Meaning, the model considers that genome assembly errors create rare spurious breakpoints between the RH map order and the current goat genome assembly order [ 12].
Equivalently, we consider that genome assembly errors create rare spurious breakpoints between the RH map order and the current assembly order.
In the course of this study, three factors emerged as evident causes of discrepancies in map orders and lengths between RG and ML methods and among families.
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