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By applying SMALT, reads which have a unique mapping position in the reference (perfect match is not necessary) are referred to as mapped reads.
We defined reads as being mapped to shifted positions, if their mapping position in reference 1 was at least within a ±10% range of the mapping position in reference 2 (read position in ref.1 +/− 10% = read position in ref. 2, see Additional file 5: Table S3).
By using diverse EST libraries of E. multilocularis (see Materials and Methods) we searched for ta-TRIM-like transcripts by BLASTN and mapped them to the genome of E. multilocularis under stringent requirements (single mapping position in the genome with greater than 99% identity to the EST).
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The primers were selected because of their map position in different maps of B. rapa and distribution over all the linkage groups (A01 A10) [33].
b Nearest marker to peak of the detected QTL and its map position (in Kosambi cM).
For 54 genes out of the 91, the map position in Pop9 confirmed previous mapping results (Additional file 2).
a QTL name (according to Miklas and Porch 2010) and its estimated map position (in Kosambi cM).
The linear function was fit to the points representing genetic and physical map position in 4 Mb windows.
For P97, only RAPD markers selected on the basis of their map position in the P93 linkage maps were used for genetic mapping with 190 individuals.
Cartesian coordinates of 127 genes/ESTs and BESs based on their map position in HSA 1, 9, and 10 in SSC10 were also developed (Fig. 2).
Given that these deficiencies are not associated with genetic locations, we converted the estimated genetic map position of our mutation (in cM) to a physical map position (in cytology) (see File S1).
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