KaTomicsDB is a portal website for the tomato genomics databases for DNA markers, SNP annotations, and genome sequences released from our research group. Refer to Shirasawa and Hirakawa (2013).
Data sets
- Genome, gene annotation, and variant files for Micro-Tom, NBRP-Japan [ Shirasawa and Ariizumi 2023 bioRixv ]
- Gene annotation files (gff, cds, and pep) for CMS tomato lines [ Kuwabara et al. 2021 Hort Res ]
- This VCF (Variant Call Format) file includes 965 SNP sites from an F2 population derived from a cross between P110 and M110. [ Safaei et al. 2020 Plant Genome ]
- This VCF (Variant Call Format) file includes 1,187,941 SNP sites from whole-genome resequencing data for Micro-Tom and Regina. [ Shirasawa et al. 2016 DNA Res ]
- This VCF (Variant Call Format) file includes 29,702 SNP sites from ddRAD-Seq data (EcoRI/HindIII, PstI/MspI, PstI/EcoRI, and SalI/PstI) for Micro-Tom and Regina. [ Shirasawa et al. 2016 DNA Res ]
- This VCF (Variant Call Format) file includes 41,909 SNP sites from ddRAD-Seq data (PstI/MspI) for 6 cultivars. [ Shirasawa et al. 2016 DNA Res ]
- This MCT (MapChart Format) file includes 1,257 SNP loci on a genetic map based on the tomato genome sequence, SL2.50. [ Shirasawa et al. 2016 DNA Res ]
- This MCT (MapChart Format) file includes 686 SNP loci on a genetic map based on a de novo assembly of RAD reads. [ Shirasawa et al. 2016 DNA Res ]
- This VCF (Variant Call Format) file includes 5,145 mutations of 4 EMS and 3 gamma-ray Micro-Tom mutants. [ Shirasawa et al. 2016 Plant Biotechnol J ]
- This VCF (Variant Call Format) file includes 1,140,687 spontaneous SNPs in Micro-Tom lines. [ Shirasawa et al. 2016 Plant Biotechnol J ]
- This HapMap file includes 1,247 SNPs genotyped with the Illumina GoldenGate array across 663 accessions. [ Shirasawa et al. 2013 DNA Research 20: 593-603 ]
- This VCF (Variant Call Format) file includes 1,473,798 SNP sites from resequencing data for 6 accessions. [ Shirasawa et al. 2013 DNA Research 20: 593-603 ]