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Detailed information for vg0302837094:

Variant ID: vg0302837094 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 2837094
Reference Allele: CAlternative Allele: T
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 304. )

Flanking Sequence (100 bp) in Reference Genome:


TAATATTGAAGCACTCATTTGATTGTATATTTTAATCATTACCTCTAATGCTTTCTGTGCCCATTTATATTAACAAGTATGCTAAATCATTATCATAGCA[C/T]
ACACTTATGAGTCTGCTGGATTCATTTTATTTTCAGGAACCCTAGAGAACTACTGTCTGGAATCCGAACTTCTCGTCTAAGAGATCGTAAAAAAGAAGAC

Reverse complement sequence

GTCTTCTTTTTTACGATCTCTTAGACGAGAAGTTCGGATTCCAGACAGTAGTTCTCTAGGGTTCCTGAAAATAAAATGAATCCAGCAGACTCATAAGTGT[G/A]
TGCTATGATAATGATTTAGCATACTTGTTAATATAAATGGGCACAGAAAGCATTAGAGGTAATGATTAAAATATACAATCAAATGAGTGCTTCAATATTA

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 96.50% 2.20% 1.31% 0.00% NA
All Indica  2759 94.00% 3.80% 2.21% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 83.40% 10.30% 6.39% 0.00% NA
Indica II  465 95.70% 2.40% 1.94% 0.00% NA
Indica III  913 100.00% 0.00% 0.00% 0.00% NA
Indica Intermediate  786 94.00% 4.20% 1.78% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 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 98.90% 0.00% 1.11% 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
vg0302837094 C -> T LOC_Os03g05690.1 upstream_gene_variant ; 1678.0bp to feature; MODIFIER silent_mutation Average:45.165; most accessible tissue: Minghui63 flower, score: 56.131 N N N N
vg0302837094 C -> T LOC_Os03g05700.1 downstream_gene_variant ; 4696.0bp to feature; MODIFIER silent_mutation Average:45.165; most accessible tissue: Minghui63 flower, score: 56.131 N N N N
vg0302837094 C -> T LOC_Os03g05680.1 intron_variant ; MODIFIER silent_mutation Average:45.165; most accessible tissue: Minghui63 flower, score: 56.131 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0302837094 4.29E-06 4.29E-06 mr1529_2 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