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Detailed information for vg0207636002:

Variant ID: vg0207636002 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 7636002
Reference Allele: CAlternative Allele: G
Primary Allele: CSecondary Allele: G

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, others allele: 0.00, population size: 309. )

Flanking Sequence (100 bp) in Reference Genome:


TACAACTAAATAGCCACAAAAGATCACCAACACTATACTGGATTATGTCAAAGAATTGCTTTTCATAGAGCCGTTAAAATCTCCGTATGCCAGAGCCGCC[C/G]
AGTCACCACTCTTATTAGCGATCTCCAATGTACTCTTATATAAGAAAACCCCAAAGAACGATATACTATCAAAAGAAAATGAGAAGATCCAAGGAAGAAG

Reverse complement sequence

CTTCTTCCTTGGATCTTCTCATTTTCTTTTGATAGTATATCGTTCTTTGGGGTTTTCTTATATAAGAGTACATTGGAGATCGCTAATAAGAGTGGTGACT[G/C]
GGCGGCTCTGGCATACGGAGATTTTAACGGCTCTATGAAAAGCAATTCTTTGACATAATCCAGTATAGTGTTGGTGATCTTTTGTGGCTATTTAGTTGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 97.10% 2.60% 0.23% 0.00% NA
All Indica  2759 99.90% 0.00% 0.07% 0.00% NA
All Japonica  1512 91.50% 7.90% 0.60% 0.00% NA
Aus  269 99.60% 0.40% 0.00% 0.00% NA
Indica I  595 99.70% 0.00% 0.34% 0.00% NA
Indica II  465 100.00% 0.00% 0.00% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 99.90% 0.10% 0.00% 0.00% NA
Temperate Japonica  767 98.70% 1.00% 0.26% 0.00% NA
Tropical Japonica  504 86.50% 12.70% 0.79% 0.00% NA
Japonica Intermediate  241 79.30% 19.50% 1.24% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 95.60% 4.40% 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
vg0207636002 C -> G LOC_Os02g13990.1 upstream_gene_variant ; 768.0bp to feature; MODIFIER silent_mutation Average:65.07; most accessible tissue: Callus, score: 81.559 N N N N
vg0207636002 C -> G LOC_Os02g13990.3 upstream_gene_variant ; 768.0bp to feature; MODIFIER silent_mutation Average:65.07; most accessible tissue: Callus, score: 81.559 N N N N
vg0207636002 C -> G LOC_Os02g13990.2 upstream_gene_variant ; 758.0bp to feature; MODIFIER silent_mutation Average:65.07; most accessible tissue: Callus, score: 81.559 N N N N
vg0207636002 C -> G LOC_Os02g13990-LOC_Os02g14000 intergenic_region ; MODIFIER silent_mutation Average:65.07; most accessible tissue: Callus, score: 81.559 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0207636002 2.13E-06 2.13E-06 mr1067_2 Jap_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
vg0207636002 NA 1.70E-06 mr1929_2 Jap_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
vg0207636002 NA 2.85E-07 mr1962_2 Jap_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