Additional file 2 of Coordinates and intervals in graph-based reference genomes

Example of gene notation. Example of representation of genes on an alternative locus on GRCh38 (txt). (TXT 4 kb

Additional file 1 of Coordinates and intervals in graph-based reference genomes

Definitions and experiment details. Formal definitions of terms used in the article and details on the section Genes on GRCh38 (pdf). (PDF 181 kb

Genotypes for Spanish sparrow reference population

Genotypes for the individuals in the spanish sparrow reference population for the 77 SNP marker

bgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatry

bgc input file for house sparrow parental population (reference population) when analysing Z-linked loci separately in parental sympatr

File to link locus names with bgc output

File showing which loci refers to which 'bgc output number' for all 77 markers, only autosomal markers and only Z-linked marker

qb.out_parental sympatry

output from BGC run on parental sympatry test population: estimates of beta parameter quantiles for the 77 loc

bgc input file for test population when analysing Z-linked loci separately in parental sympatry

bgc input file for test population when analysing Z-linked loci separately in parental sympatr

bgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatry

bgc input file for Spanish sparrow parental population (reference population) when analysing autosomal loci separately in parental sympatr

structure_input_file

'structure_input.txt': input file used when running structure. numbers in second column refer to: 1: house sparrows from Oslo, Norway 2: house sparrows from Hradec Králové, Czech Republic 3: house sparrows from sympatric population near Badajoz, Spain 4: Spanish sparrows from sympatric population near Badajoz, Spain 5: Spanish sparrows from the Gargano Peninsula 6: Spanish sparrows from Sardinia 7: F1-hybrids from aviar

b.out_hybrid-parents analysis

output from BGC: estimates of cline parameter beta for 77 the loci used in the hybrid-parents analysi