2.1.4 QTL Table
As for GLMdb the QTL database consists of as many plain text files as the number of mapping experiments described in the experiment table. Each file must respect the same naming convention as for GLMdb, i.e the stem name of the file must be the name of the corresponding mapping experiment as defined in the map field of the experiment table. Thus if QTL detection result have been obtained for the mapping experiments exp1 we will have a exp1.qtl file (for the QTL results) and a exp1.map (for the genetic linkage map used to map the QTL). Each file of QTLdb must contain the following fields:
- group (string) : the linkage group name.
- qtl (string) : the name of the QTL.
- position (numeric) : the most probable position of the QTL on the linkage group.
- qtl.trait.name(string): the name of the trait for which this QTL has been detected.
- qtl.ic.from (numeric) : the lower bound of the CI of the QTL position.
- qtl.ic.to (numeric) : the upper bound of the CI of the QTL position.
- qtl.ic.lod.decrease(numeric): if the CI is based on a LOD support used this field to define the decrease of LOD which was used to build the CI.
- qtl.rsquare(numeric): the estimated r-square of the QTL.
- qtl.cross.name(string): the name of the cross used to carry out the QTL mapping.
- qtl.cross.type(string): the type of the cross used to carry out the QTL mapping.
- qtl.cross.size(integer): the size of the cross used to carry out the QTL mapping.
The fields in bold are required while those in italic are optional.
group locus position type qtl.ic.lod.decrease qtl.ic.from qtl.ic.to qtl.rsquare \
qtl.effect.addtive qtl.trait.name
1 QTL1 208 Q 1 182 236 0.044 days_to_pollen
1 QTL2 152 Q 1 128 174 0.045 anthesis_silking
2 QTL3 74 Q 1 58 88 0.051 anthesis_silking
2 QTL4 126 Q 1 110 140 0.048 days_to_silk
3 QTL6 36 Q 1 18 46 0.093 kernel_weight
2 QTL5 76 Q 1 60 92 0.061 kernel_weight
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