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Detailed information for vg0723222806:

Variant ID: vg0723222806 (JBrowse)Variation Type: SNP
Chromosome: chr07Position: 23222806
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:


TATCTCTCACTTATACATTTAATGTATTTGTCTTGAACCTTGTGATAAGTTAGCTCTTGCATGAGAGCCAACATCCTTAATTTTTCACTACCTCTCTCCT[C/T]
CACCTAAGCTTATAGTATGCTTATAGCTCACTATTATACTTGCTCTTATGCTACTAGTACGTACTACTGTAGTTTGCAATTTGCAGTGTTTTCTTTCTTC

Reverse complement sequence

GAAGAAAGAAAACACTGCAAATTGCAAACTACAGTAGTACGTACTAGTAGCATAAGAGCAAGTATAATAGTGAGCTATAAGCATACTATAAGCTTAGGTG[G/A]
AGGAGAGAGGTAGTGAAAAATTAAGGATGTTGGCTCTCATGCAAGAGCTAACTTATCACAAGGTTCAAGACAAATACATTAAATGTATAAGTGAGAGATA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 86.70% 13.00% 0.28% 0.00% NA
All Indica  2759 83.40% 16.10% 0.43% 0.00% NA
All Japonica  1512 99.90% 0.10% 0.00% 0.00% NA
Aus  269 40.50% 59.10% 0.37% 0.00% NA
Indica I  595 96.80% 2.00% 1.18% 0.00% NA
Indica II  465 82.20% 17.80% 0.00% 0.00% NA
Indica III  913 79.00% 21.00% 0.00% 0.00% NA
Indica Intermediate  786 79.30% 20.10% 0.64% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 90.00% 10.00% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0723222806 C -> T LOC_Os07g38670.1 upstream_gene_variant ; 309.0bp to feature; MODIFIER silent_mutation Average:61.106; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0723222806 C -> T LOC_Os07g38690.1 upstream_gene_variant ; 4578.0bp to feature; MODIFIER silent_mutation Average:61.106; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0723222806 C -> T LOC_Os07g38664.1 downstream_gene_variant ; 1855.0bp to feature; MODIFIER silent_mutation Average:61.106; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0723222806 C -> T LOC_Os07g38680.1 downstream_gene_variant ; 3026.0bp to feature; MODIFIER silent_mutation Average:61.106; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N
vg0723222806 C -> T LOC_Os07g38664-LOC_Os07g38670 intergenic_region ; MODIFIER silent_mutation Average:61.106; most accessible tissue: Zhenshan97 panicle, score: 84.374 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0723222806 6.39E-06 1.63E-08 mr1376 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0723222806 6.39E-06 1.63E-08 mr1431 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0723222806 NA 1.79E-06 mr1830 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0723222806 NA 4.96E-06 mr1570_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251