Warning!
This website will be shut down on December 10, 2026, as its mission is now complete. All contents have been integrated into our new database, Kazusa Genome Atlas. See you there again, stepping forward into the future!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 ]