SNPs_publication_ATCG

file 1: 'SNPs_publication_ATCG': this file contains the raw SNPs database in GenAlEx format for two sets of samples (sheets 1 and 2): sheet 1: SNPs data for all 274 cat samples used in the analyses (139 domestic cats - FCA; 130 putative European wildcats - FSI; 5 known hybrids FCA x FSI), characterised by 158 loci; sheet 2: SNPs data for 226 cat samples (139 domestic cats - FCA; 82 European wildcats - FSI; 5 known hybrids FCA x FSI), characterised by 158 loci. This sample set was created to exclude possible hybrids from the representatives of European wildcats. These files can be converted to other formats using GenAlEx

Additional file 3: Figure S2. of Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

Sequencing Reads in the Persian Cat Trio. Quality assessment (removing low quality bases, trimming adapters and subsequently excluding reads under 20 bases) reduced the number of reads for each library and lane. Fewer reads were generated from 550 base pair libraries (those containing the text “Lib550”). The unique read counts displayed here were calculated by FastQC; duplicates reported in the text were calculated from marked duplicates among mapped reads. a) Cat 13230 non-carrier queen, b) Cat 14056 affected sire, and c) Cat 16628 carrier offspring. (ZIP 229 kb

Additional file 4: Figure S3. of Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

Bases within a Given Depth of Sequence for WGS Persian Cats. The red and green lines represent the average coverage of the parents (S13230 and S14056) and the blue line represents the average coverage of the offspring (S16628). (PNG 253 kb

Additional file 2: Figure S1. of Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

Representative Base Quality Scores of Untrimmed Sequencing Reads for the Persian cat trio. Base-specific quality scores were aggregated and plotted using FastQC (already cited, 27 and 29). Phred-scaled quality scores (y axis) are plotted against base position within the read (x axis). Box spans second and third quartiles; whiskers indicate 10th and 90th percentiles. Median and mean are plotted as red and blue lines respectively. The data aggregated here represents end X of untrimmed reads from a single library data in a single lane. (PNG 15 kb

Additional file 5: Figure S4. of Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

AIPL1 Protein Sequence Alignments. Presented are sequences for Homo sapiens, Mus musculus, Felis silvestris catus and Felis silvestris catus with the identified mutation. In green, blue, purple and grey sequences of different domains inferred using the Homo sapiens domain protein annotation ( www.uniprot.org ). In yellow, residues that differ between the Homo sapiens and Mus musculus when compared to the feline protein sequence. The AIPL1 feline mutated sequence lacks partial TRP1 and TRP2 and TRP3. (DOCX 151 kb

Additional file 1: Table S1. of Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7

AIPL1 c.577C > T and HES7 c.5A > G Genotypes in Domestic Cats. Table S2. Primer Sequences for the Analysis of AIPL1 in Domestic Cats. Table S3. Genome Coverage of Persian Cat PRA Trio. (DOCX 32 kb