2.1.4 QTLdb

As for GLMdb the QTL database consists in 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 a QTL detection result has been reported for the mapping experiment `exp1' we will have a file exp1.txt. Each file of QTLdb are organized as follows:

• 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 to which this QTL is related.
• qtl.ci.from(numeric) : the lower bound of the CI of the QTL position.
• qtl.ci.to(numeric) : the upper bound of the CI of the QTL position.
• qtl.ci.lod.decrease(numeric): if the CI is based on a LOD support, use 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.

group qtl position qtl.ci.lod.decrease qtl.ci.from qtl.ci.to qtl.rsquare qtl.trait.name 1 QTL1 208 1 182 236 0.044 days_to_pollen_shed 1 QTL2 152 1 128 174 0.045 silking_date 2 QTL3 74 1 58 88 0.051 silking_date 2 QTL4 126 1 110 140 0.048 days_to_pollen_shed 3 QTL6 36 1 18 46 0.093 leaf_number 8 QTL5 76 1 60 92 0.21 leaf_number