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Detailed information for vg0200790778:

Variant ID: vg0200790778 (JBrowse)Variation Type: SNP
Chromosome: chr02Position: 790778
Reference Allele: AAlternative Allele: C
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, A: 0.03, others allele: 0.00, population size: 209. )

Flanking Sequence (100 bp) in Reference Genome:


GAGCTAGACTCTATGTACTGTAATGCTTTTGTTATTATTTTGGAAAAAAAAGGGTGAGAATTCTTCCTTGGCTGGAATTTCAACTGGCCTAAGAATTGTG[A/C]
TCAAGCTAAGCTTGAACTAACCCAAAGCTAAGTACTCTCTGTAACTGCTAATTACCAATTAGAGAGGGGACTAGACTAGGCTAGAATTCACAATTGTGAA

Reverse complement sequence

TTCACAATTGTGAATTCTAGCCTAGTCTAGTCCCCTCTCTAATTGGTAATTAGCAGTTACAGAGAGTACTTAGCTTTGGGTTAGTTCAAGCTTAGCTTGA[T/G]
CACAATTCTTAGGCCAGTTGAAATTCCAGCCAAGGAAGAATTCTCACCCTTTTTTTTCCAAAATAATAACAAAAGCATTACAGTACATAGAGTCTAGCTC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 78.50% 21.40% 0.04% 0.00% NA
All Indica  2759 98.50% 1.40% 0.04% 0.00% NA
All Japonica  1512 44.60% 55.40% 0.00% 0.00% NA
Aus  269 63.20% 36.80% 0.00% 0.00% NA
Indica I  595 99.30% 0.70% 0.00% 0.00% NA
Indica II  465 97.80% 2.20% 0.00% 0.00% NA
Indica III  913 99.70% 0.30% 0.00% 0.00% NA
Indica Intermediate  786 96.90% 2.90% 0.13% 0.00% NA
Temperate Japonica  767 17.30% 82.70% 0.00% 0.00% NA
Tropical Japonica  504 90.50% 9.50% 0.00% 0.00% NA
Japonica Intermediate  241 35.70% 64.30% 0.00% 0.00% NA
VI/Aromatic  96 84.40% 14.60% 1.04% 0.00% NA
Intermediate  90 75.60% 24.40% 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
vg0200790778 A -> C LOC_Os02g02360.1 downstream_gene_variant ; 1543.0bp to feature; MODIFIER silent_mutation Average:61.345; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790778 A -> C LOC_Os02g02380.1 downstream_gene_variant ; 4288.0bp to feature; MODIFIER silent_mutation Average:61.345; most accessible tissue: Callus, score: 86.638 N N N N
vg0200790778 A -> C LOC_Os02g02370.1 intron_variant ; MODIFIER silent_mutation Average:61.345; most accessible tissue: Callus, score: 86.638 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0200790778 NA 2.58E-06 mr1092 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
vg0200790778 NA 8.64E-07 mr1154 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
vg0200790778 NA 8.28E-06 mr1330_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
vg0200790778 NA 3.06E-08 mr1347_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
vg0200790778 NA 3.88E-06 mr1606_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