QTL database for "Genomic underpinnings of head and body shape in Arctic charr ecomorph pairs" by Sam Fenton, Arne Jacobs, Colin W. Bean, Colin E. Adams, & Kathryn R. Elmer
published in Molecular Ecology

The folder contains two files related to the QTL database: 
-All_collected_QTL_markers file contains information on all the QTL markers collected for the database
-Mapped_QTL_marker_positions contains information on mapped locations for all successfully mapped markers

Each QTL marker is given a ID (species_phenotype_number) with each species and trait given a unique code. Information on the original linkage group the QTL marker mapped to for the genome used in the original paper along with peak position, type of confidence interval (and their range), and proportion of variance explained. The original marker name is provided before the sequence information needed to map the QTLs. 

Sequence used to map the QTLs to the Salvelinus sp. genome are provided in the respective column based on the QTL type (e.g. RAD-tag QTLs). Single long sequence such as the RADtag markers were mapped using Bowtie2 while the microsatellite markers with Bowtie1 using settings described in our paper. All available sequences for a marker were mapped to the genome where relevant (for example where forward and reverse and/or left and right marker sequences are provided). Markers that had sequences mapping to different chromosomes were filtered out of the mapped database as described in the paper. 

In the mapped positions file, the successfully mapped QTLs are split by the pipeline they were run in (Bowtie2/Bowtie1). Chromosome/scaffold the QTL marker mapped to in the Salvelinus sp. genome and peak position is provided for each marker. For the shorter sequences (broadly called microsat QTLs in the database for convenience), each successfully mapped sequence is shown as a separate entry. A suffix is added to identify which sequence this is for the respective QTL marker(e.g. Oki_BL_009_left_r is the left flanking reverse sequence for marker Oki_BL_009). Where multiple different markers from the same species for the same trait mapped to the same position, the one with highest PVE was kept.