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The "first-order" and "compare" commands were then used to identify the most probable marker order within a linkage group.
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The relative position of each accessory marker to its most probable framework marker was then provided using the two-point LOD scores and recombination fractions available in the "maximum linkage" table of JoinMap.
The position of each accessory marker relative to its most probable framework marker was then determined from the two-point LOD scores and recombination fractions provided by the "maximum linkage" table of JoinMap.
Accessory test-cross (56 and 82 loci for G2F and G2M, respectively) or intercross (409 loci) markers were localized to their most probable framework marker location (indicated in blue in Figure 2 and Additional file 3).
Most probable order of marker inside each LG was estimated using the "flipsn" option.
It was not possible to distinguish whether there are two linked QTL, one affecting CM and the other affecting yield, or one pleiotropic QTL affecting both CM and yield traits in DR. Vilkki et al. (1997) identified a QTL on BTA9 affecting milk and protein yield in FA cattle, with the most probable location near the marker UWCA9 (equivalent to 40.4 cM of our map).
The most probable source of cartilage markers in knee-joint fluid is the PF or TF joints.
In relationship testing the aim is to determine the most probable pedigree structure given genetic marker data for a set of persons.
Also, most likely because of the limited of markers, the most probable location of the five QTL was identified with relatively large 95% confidence intervals.
Once the mungbean whole genome sequence became available [ 7], the sequences of the SSR primers were mapped to the genome sequence using blast.2.2.27+ [ 32] to determine the most probable chromosomal location of the markers.
In families 1 and 2, with the dam originating from a clonal line and by inferring the most probable phase of the genetic markers of the sire, the cross had the same properties as a backcross and was analysed as such.
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