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Inconsistencies in chromosome lengths and marker order led to different chromosome genetic lengths.
However, inconsistencies in marker order led to difficulties in integrating around one third of these QTLs.
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Missing data complicated the computation of reliable marker ordering and sequencing artifacts led to a high number of perceived double recombination events per individual following initial map construction.
SNP whose inclusion led to large distortions in marker order were discarded.
Although the RAPD markers could have been integrated, trying to pack in a very large number of markers could lead to a reduced likelihood support for marker order of the microsatellites, main focus of this study.
The order, but not the distance between markers, was conserved between populations and is consistent with the marker order along the rice pseudomolecules (TIGR v.5, www.gramene.org).org
Similar to the ripple command that is used to determine marker order, a sliding window analysis also reveals the reliability of the marker order, by comparing the likelihood of the most likely marker order with alternative orders (flips test).
The process of switching the order of marker pairs was repeated to finalize marker order.
The FLIPS5 function was used to shuffle marker orders and identify the most likely marker order.
MergeMap calculates a consensus marker order based on the marker order from individual maps.
MergeMap takes into account marker order from individual maps and calculates a consensus marker order.
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