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Detailed information for vg0402029490:

Variant ID: vg0402029490 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 2029490
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.02, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

CAACTCTGGGTCTTGTTTGCTGTTTTCATTACTATACATATGTTTGTGGAAACACAAACCGTTAAGAGTGTGTAACTAATTTAAAACTGTGACGACCAGG[G/A]
TTCGCAAAAACCATTGGGGATAGACAATTCATGCGCCAACAAGATAGAGAGTTCACATGCACGTATGGACTTGATAATTCGTTGTAAGATGCACAACGGA

Reverse complement sequence

TCCGTTGTGCATCTTACAACGAATTATCAAGTCCATACGTGCATGTGAACTCTCTATCTTGTTGGCGCATGAATTGTCTATCCCCAATGGTTTTTGCGAA[C/T]
CCTGGTCGTCACAGTTTTAAATTAGTTACACACTCTTAACGGTTTGTGTTTCCACAAACATATGTATAGTAATGAAAACAGCAAACAAGACCCAGAGTTG

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	81.70%	18.20%	0.08%	0.00%	NA
All Indica	2759	83.20%	16.70%	0.11%	0.00%	NA
All Japonica	1512	81.10%	18.90%	0.00%	0.00%	NA
Aus	269	72.50%	27.50%	0.00%	0.00%	NA
Indica I	595	87.60%	12.40%	0.00%	0.00%	NA
Indica II	465	94.20%	5.80%	0.00%	0.00%	NA
Indica III	913	72.40%	27.40%	0.22%	0.00%	NA
Indica Intermediate	786	85.90%	14.00%	0.13%	0.00%	NA
Temperate Japonica	767	96.20%	3.80%	0.00%	0.00%	NA
Tropical Japonica	504	60.10%	39.90%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	67.70%	31.20%	1.04%	0.00%	NA
Intermediate	90	87.80%	12.20%	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
vg0402029490	G -> A	LOC_Os04g04330.1	upstream_gene_variant ; 4960.0bp to feature; MODIFIER	silent_mutation	Average:51.953; most accessible tissue: Callus, score: 82.557	N	N	N	N
vg0402029490	G -> A	LOC_Os04g04330.2	upstream_gene_variant ; 4983.0bp to feature; MODIFIER	silent_mutation	Average:51.953; most accessible tissue: Callus, score: 82.557	N	N	N	N
vg0402029490	G -> A	LOC_Os04g04320.1	downstream_gene_variant ; 3046.0bp to feature; MODIFIER	silent_mutation	Average:51.953; most accessible tissue: Callus, score: 82.557	N	N	N	N
vg0402029490	G -> A	LOC_Os04g04320.2	downstream_gene_variant ; 3046.0bp to feature; MODIFIER	silent_mutation	Average:51.953; most accessible tissue: Callus, score: 82.557	N	N	N	N
vg0402029490	G -> A	LOC_Os04g04320-LOC_Os04g04330	intergenic_region ; MODIFIER	silent_mutation	Average:51.953; most accessible tissue: Callus, score: 82.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0402029490	6.33E-07	NA	mr1798	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
vg0402029490	2.54E-10	NA	mr1798_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
vg0402029490	6.35E-06	NA	mr1798_2	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
vg0402029490	3.42E-06	NA	mr1798_2	Jap_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