Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0308391272:

Variant ID: vg0308391272 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8391272
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

AACAGCCTCTTTAACATGCACAGGGAAATTTTACTTAACTAGGGAAATTTCACACCCCAATCCGGTACCACCGTACAACGATACCTGATAGGAGCGTGTC[G/A]
TAGGAAAAACGGTGCGAACCGCTTCCTATGAGACCGCGATCTCAGTACCAGTCCCAGGACATAGCGCTGGTACCCACGGTGACAAATATGAATCATTGCA

Reverse complement sequence

TGCAATGATTCATATTTGTCACCGTGGGTACCAGCGCTATGTCCTGGGACTGGTACTGAGATCGCGGTCTCATAGGAAGCGGTTCGCACCGTTTTTCCTA[C/T]
GACACGCTCCTATCAGGTATCGTTGTACGGTGGTACCGGATTGGGGTGTGAAATTTCCCTAGTTAAGTAAAATTTCCCTGTGCATGTTAAAGAGGCTGTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.20%	0.50%	0.34%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	97.40%	1.60%	1.06%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	95.00%	2.90%	2.09%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0308391272	G -> A	LOC_Os03g15330.1	upstream_gene_variant ; 4217.0bp to feature; MODIFIER	silent_mutation	Average:64.623; most accessible tissue: Callus, score: 83.582	N	N	N	N
vg0308391272	G -> A	LOC_Os03g15330-LOC_Os03g15340	intergenic_region ; MODIFIER	silent_mutation	Average:64.623; most accessible tissue: Callus, score: 83.582	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308391272	3.07E-06	9.50E-08	mr1968_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