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Detailed information for vg0326930070:

Variant ID: vg0326930070 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 26930070
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.76, T: 0.25, others allele: 0.00, population size: 245. )

Flanking Sequence (100 bp) in Reference Genome:

ATGGCGGTTGAGGGGTACTTCGGACAATTCCCCTTCCACAACCATCATAACCACCTCTTTATAAGGAGCTCACTCTCTTCACTTAAAGACACACCTCAAG[C/T]
AAGAGCTCTCTCATTCCTCTCAAGTTTAGTTTAGTAGTATCTAGCTGGTGGAATAGAATTAGAATAGGAATCAGGAGTCCGAAAGTCTTCGGAAGAGTTC

Reverse complement sequence

GAACTCTTCCGAAGACTTTCGGACTCCTGATTCCTATTCTAATTCTATTCCACCAGCTAGATACTACTAAACTAAACTTGAGAGGAATGAGAGAGCTCTT[G/A]
CTTGAGGTGTGTCTTTAAGTGAAGAGAGTGAGCTCCTTATAAAGAGGTGGTTATGATGGTTGTGGAAGGGGAATTGTCCGAAGTACCCCTCAACCGCCAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.70%	38.30%	0.00%	0.00%	NA
All Indica	2759	93.50%	6.50%	0.00%	0.00%	NA
All Japonica	1512	1.20%	98.80%	0.00%	0.00%	NA
Aus	269	96.30%	3.70%	0.00%	0.00%	NA
Indica I	595	83.70%	16.30%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.50%	1.50%	0.00%	0.00%	NA
Indica Intermediate	786	92.50%	7.50%	0.00%	0.00%	NA
Temperate Japonica	767	0.50%	99.50%	0.00%	0.00%	NA
Tropical Japonica	504	1.80%	98.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	14.60%	85.40%	0.00%	0.00%	NA
Intermediate	90	47.80%	52.20%	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
vg0326930070	C -> T	LOC_Os03g47584.1	upstream_gene_variant ; 3681.0bp to feature; MODIFIER	silent_mutation	Average:38.498; most accessible tissue: Zhenshan97 flower, score: 54.272	N	N	N	N
vg0326930070	C -> T	LOC_Os03g47590.1	upstream_gene_variant ; 4623.0bp to feature; MODIFIER	silent_mutation	Average:38.498; most accessible tissue: Zhenshan97 flower, score: 54.272	N	N	N	N
vg0326930070	C -> T	LOC_Os03g47584-LOC_Os03g47590	intergenic_region ; MODIFIER	silent_mutation	Average:38.498; most accessible tissue: Zhenshan97 flower, score: 54.272	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0326930070	NA	5.18E-13	mr1701	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
vg0326930070	NA	2.69E-11	mr1713	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
vg0326930070	NA	4.48E-19	mr1754	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
vg0326930070	NA	7.88E-10	mr1322_2	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
vg0326930070	NA	5.12E-22	mr1336_2	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
vg0326930070	NA	5.78E-17	mr1579_2	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