Tomato Genotype Data

Tomato Sanger SNP Survey

Tomato Intervarietal SNPs

Tomato Illumina Validation SNPs

Tomato Infinium SNP Annotation

Manufacturing Quality: This column indicates whether the SNP passed Illumina's production quality control. "PASS" indicates the SNP can be scored in the current bead pool (7,720 SNPs). The SNPs with "FAIL" in this column did not pass manufacturing qc due to normal failures which are expected to be less than 15%, faulty SNP design, or both.

Data quality: This column indicates how well the SNP was scored in the SolCAP germplasm panel. "Excellent" indicates that less than 10% of accessions had ambiguous scores for the SNP; "Moderate" indicates that 10-20% of accessions had ambiguous or missing scores; "Poor" indicates that greater than 20% of accessions had ambiguous or missing scores; "Missing" indicates that the SNP could not be scored.

Chromosome and SNP position: These columns indicate the physical map location of the SNP based on the Tomato WGS chromosome database (SL2.40) at SGN. To obtain this information, the flanking sequences of the SNP were oriented relative to the genome sequence using BLAST, and the position of the SNP was determined relative to the query start/end using a custom python script. "SNP position" indicates the actual SNP position relative to the Tomato WGS chromosome database (SL2.40).

Tomato Infinium Manifest File - The manifest file describes the SNP or probe content on the SolCAP Infinium Chip.

Tomato Infinium Cluster File - Infinium chip cluster file based on the SolCAP tomato collection.