Additional file 1: of Comparative analysis of the chicken IFITM locus by targeted genome sequencing reveals evolution of the locus and positive selection in IFITM1 and IFITM3

Table S1. List of the inbred lines from the Pirbright Institute (Adapted from http://www.narf.ac.uk/chickens/lines.html ). The table shows a list of all the inbred lines from the Pirbright Institute together with relevant information regarding each line. ENA ID is provided for each group. Table S2. List of the European chicken breeds. The table shows a list of all the European breeds and their origin (muscle or blood). ENA ID is provided for each group. Table S3. List of the commercial chickens purchased across UK. The table shows a list of all the supermarket-derived chicken breast purchased between Cambridge, Saffron Walden and Cambourne in 2016. Chickens were also classified based on their origin: standard, free range or organic. ENA ID is provided for each group. Table S4. List of the indigenous chickens from Nigeria and Ethiopia. The table shows a list of all the indigenous chickens from Nigeria and Ethiopia. Additional information regarding the village of origin is shown. ENA ID is provided for each group. Figure S1. IGV SNVs view and density across the 40Kb region. The VCF file generated by GATK was uploaded using IGV. The figure shows a snapshot of the full-length locus, including the flanking genes ATHL1 and B4GALNT4. Samples showing high levels of heterozygosity are highlighted on the right side of the figure. Blue: SNVs heterozygous for the alternate allele, cyan: SNVs homozygous for the alternate allele, grey: SNVs homozygous for the reference allele, white: no call from GATK. A.: European breeds, B.: commercial chickens from UK supermarkets. C.: inbred lines from the Pirbright Institute, D.: indigenous chickens from Ethiopia and Nigeria. Refer to Tables S1-S4 for additional for information about the single samples. (PDF 5254 kb