Marker Placement Types

MapMaker version 3.0 was used to construct these genetic linkage maps. For a detailed explanation of the program see the online Mapmaker manual. To download Mapmaker or other WIBR/MIT CGR software go to the Genome Center FTP software archive.

LOD scores listed in the marker placement descriptions below are derived as follows: Mapmaker places a marker in the interval within the framework map with the greatest likelihood. Other possible placement intervals are then assigned a likelihood score relative to this "best placement" interval. In other words, the LOD score represents how much less-likely the next best placement interval(s) is/are with regard to the best placement. If a marker's next best placement is more than 100 times less-likely (LOD>2.0) then it is considered to be placed correctly and in a unique interval. If there are other possible placement intervals that are less than 100 times less-likely (LOD<2.0) than the best placement interval, then it is somewhat likely that the marker may not be placed within the correct interval and therefore it is considered to be ambiguously placed or "bouncy". Further explanations follow:

Markers in blue type are framework loci. Markers are assigned framework status if; one) they have complete data for all critical recombinants in that region of the chromosome, two) there is a high degree of confidence in that data based on the quality of the autorad image and three) they place unique to one interval because the next most likely interval is >100 times (LOD >2.0) less-likely than the best placement interval. Each recombinationally inseperable "bin" of markers has a maximum of one framework representative.

Here is an example of one such marker: D15Rat55 (R0078-D08) Film # F07404.

Markers in green type are unique placement loci uniquely placed in one interval as the next most likely interval is >100 times (LOD >2.0) less-likely than the best placement interval.

Here is an example of one such marker: D15Rat27 (R0007-B10) Film # F01064.

Markers in black type are "bouncy" placement loci that have multiple possible placement intervals determined as such because each alternative placement interval(s) are <100 times less-likely than the best placement interval. Currently they are placed in their most likely position (which may be incorrect). This situation often arises from the absence of a critical recombinant or because of poor data quality introducing potentially erroneous or ambiguous data.

Here is an example of one such marker: D15Rat39 (R0064-B02) Film # F05908.


Robert Steen
Last modified: Fri Dec 4 12:19:09 EST