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Detailed information for vg0230481430:

Variant ID: vg0230481430 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30481430
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.62, T: 0.40, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

CAAATTAACCCAACAACTTTTGTAACCTAAAAAAGCTTACAAAAATGGTATAACACCTTTCTGTCAGGCACATTTTCATGTGCATCATAATAATTCCAAA[T/G]
AATTATTGAATCGCGTTAAAAAGGATTTTAACAGCATCGGGCCGCATCATTGTGAGCACATATTGCCAAAGCAAAAAGCGCCTAAGTCCCTAGGGATCAC

Reverse complement sequence

GTGATCCCTAGGGACTTAGGCGCTTTTTGCTTTGGCAATATGTGCTCACAATGATGCGGCCCGATGCTGTTAAAATCCTTTTTAACGCGATTCAATAATT[A/C]
TTTGGAATTATTATGATGCACATGAAAATGTGCCTGACAGAAAGGTGTTATACCATTTTTGTAAGCTTTTTTAGGTTACAAAAGTTGTTGGGTTAATTTG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	59.00%	40.80%	0.23%	0.00%	NA
All Indica	2759	91.90%	7.70%	0.36%	0.00%	NA
All Japonica	1512	0.30%	99.70%	0.00%	0.00%	NA
Aus	269	80.70%	19.00%	0.37%	0.00%	NA
Indica I	595	97.30%	2.20%	0.50%	0.00%	NA
Indica II	465	86.70%	12.90%	0.43%	0.00%	NA
Indica III	913	92.70%	7.20%	0.11%	0.00%	NA
Indica Intermediate	786	90.10%	9.40%	0.51%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	0.00%	100.00%	0.00%	0.00%	NA
Japonica Intermediate	241	1.20%	98.80%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	31.10%	68.90%	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
vg0230481430	T -> G	LOC_Os02g49890.1	upstream_gene_variant ; 399.0bp to feature; MODIFIER	silent_mutation	Average:54.068; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0230481430	T -> G	LOC_Os02g49900.1	downstream_gene_variant ; 3660.0bp to feature; MODIFIER	silent_mutation	Average:54.068; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N
vg0230481430	T -> G	LOC_Os02g49880-LOC_Os02g49890	intergenic_region ; MODIFIER	silent_mutation	Average:54.068; most accessible tissue: Minghui63 flag leaf, score: 82.75	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0230481430	NA	5.60E-06	mr1129	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
vg0230481430	NA	6.62E-07	mr1599	Ind_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