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Detailed information for vg0500881578:

Variant ID: vg0500881578 (JBrowse)Variation Type: SNP
Chromosome: chr05Position: 881578
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: 209. )

Flanking Sequence (100 bp) in Reference Genome:


AGCTGTTTTTATATAGGAAGTGTTGCCCACCTGCAATCCTATCTGCTATGATCAATGTTTTGGCAGCAAAATCTACGGTGAGCTTTAGCGCTATTCCCTC[C/T]
GTCCCAAAATATAAGAAGTTTTGGTTGGATAAGACACTTTCTGATGTCTCGTAGTACTGGGATGTATCTTATTTCAGCTAAACTTCTTATATTTTAAGAT

Reverse complement sequence

ATCTTAAAATATAAGAAGTTTAGCTGAAATAAGATACATCCCAGTACTACGAGACATCAGAAAGTGTCTTATCCAACCAAAACTTCTTATATTTTGGGAC[G/A]
GAGGGAATAGCGCTAAAGCTCACCGTAGATTTTGCTGCCAAAACATTGATCATAGCAGATAGGATTGCAGGTGGGCAACACTTCCTATATAAAAACAGCT

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 79.90% 20.00% 0.11% 0.00% NA
All Indica  2759 81.30% 18.50% 0.18% 0.00% NA
All Japonica  1512 80.20% 19.80% 0.00% 0.00% NA
Aus  269 78.80% 21.20% 0.00% 0.00% NA
Indica I  595 97.30% 2.70% 0.00% 0.00% NA
Indica II  465 85.20% 14.80% 0.00% 0.00% NA
Indica III  913 69.20% 30.20% 0.55% 0.00% NA
Indica Intermediate  786 80.90% 19.10% 0.00% 0.00% NA
Temperate Japonica  767 89.60% 10.40% 0.00% 0.00% NA
Tropical Japonica  504 81.50% 18.50% 0.00% 0.00% NA
Japonica Intermediate  241 47.30% 52.70% 0.00% 0.00% NA
VI/Aromatic  96 35.40% 64.60% 0.00% 0.00% NA
Intermediate  90 83.30% 16.70% 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
vg0500881578 C -> T LOC_Os05g02530.1 upstream_gene_variant ; 950.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500881578 C -> T LOC_Os05g02540.1 upstream_gene_variant ; 2125.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500881578 C -> T LOC_Os05g02550.1 downstream_gene_variant ; 3458.0bp to feature; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N
vg0500881578 C -> T LOC_Os05g02530-LOC_Os05g02540 intergenic_region ; MODIFIER silent_mutation Average:4.21; most accessible tissue: Minghui63 panicle, score: 7.125 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0500881578 NA 3.07E-06 mr1346 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
vg0500881578 4.06E-06 2.34E-07 mr1346 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