Database of Mytilus sp. genotyping data.
- ind: name of the individual.
- pop: population of origin.
- seq: in which sequencing or genotyping experiment the individual was genotyped.
- then one marker per column: NG = not genotyped in the experiment; NA = missing data; format allele1/allele2.
- number: numeric id of the SNP.
- name: name of the SNP.
- alt_name: multiple alternative names for the marker in case this was used in older experiments, separated by "/". Use grep style functions to search.
- sequence: flanking sequence with SNP information, e.g. [A/T].
- SNP: variants of the SNP, e.g. [A/T].
- LGC_SNPNum: LGC company internal SNP id for KASParray genotyping. A SNP can have multiple ids, separated by "/".
- LGC_AlleleX: LGC company Allele for X fluorescence.
- LGC_AlleleY: LGC company Allele for Y fluorescence.
- LGC_Sequence: LGC company internal sequence around the SNP.
- contig: Contig name from Fraïsse et al. 2016 paper.
- position: position on the contig.
- ancestry_info: see Fraïsse et al. 2016, populations this SNP differentiate.
- func: functional annotation from Fraïsse et al. 2016.
- subfunc: fubfunctional annotation from Fraïsse et al. 2016.
- gene: gene annotation from Fraïsse et al. 2016.
- comment: additional comment.
- pop: population name.
- lat: latitude.
- long: longitude.
- locality: details on the locality of the population.
- source: providers of the samples.
- collection_date: collection date when available.
- dna_extraction: DNA extraction method used.
- seq: in which sequencing or genotyping experiment the population was present. Can be multiple experiments separated by "/".
- num: number associated with population in the Beadxpress experiment.
- old_num: old number of population in the Beadxpress experiment.
- old_name: old name of population in the Beadxpress experiment.
- notes: additional notes.
- publication: in which publication this population was first used.
Fraïsse, C., Belkhir, K., Welch, J. J., & Bierne, N. (2016). Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels. Molecular Ecology, 25(1), 269–286. https://doi.org/10.1111/mec.13299