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Detailed information for vg0406998246:

Variant ID: vg0406998246 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 6998246
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.66, G: 0.35, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GAACTGCAAAGCCACACTAATAATTATATGCATTGGAACTATTTCTATTTAATTAAGGACACATTGGAATACATAGAATGGCTTGATGACACAAATCCTA[G/A]
ATGATTCATTATATATATATGTGATACCATATACAGTTTGACTCGTAAGATGGATCAACGTGCTCTTAGGAAGCATAAACCCATTAAGTTACAAAGATAT

Reverse complement sequence

ATATCTTTGTAACTTAATGGGTTTATGCTTCCTAAGAGCACGTTGATCCATCTTACGAGTCAAACTGTATATGGTATCACATATATATATAATGAATCAT[C/T]
TAGGATTTGTGTCATCAAGCCATTCTATGTATTCCAATGTGTCCTTAATTAAATAGAAATAGTTCCAATGCATATAATTATTAGTGTGGCTTTGCAGTTC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	53.40%	46.50%	0.13%	0.00%	NA
All Indica	2759	78.30%	21.60%	0.11%	0.00%	NA
All Japonica	1512	1.10%	98.90%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	95.00%	5.00%	0.00%	0.00%	NA
Indica II	465	64.90%	34.60%	0.43%	0.00%	NA
Indica III	913	75.10%	24.90%	0.00%	0.00%	NA
Indica Intermediate	786	77.10%	22.80%	0.13%	0.00%	NA
Temperate Japonica	767	0.30%	99.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.80%	98.20%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.50%	0.41%	0.00%	NA
VI/Aromatic	96	44.80%	55.20%	0.00%	0.00%	NA
Intermediate	90	40.00%	57.80%	2.22%	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
vg0406998246	G -> A	LOC_Os04g12620.1	upstream_gene_variant ; 2942.0bp to feature; MODIFIER	silent_mutation	Average:38.888; most accessible tissue: Callus, score: 65.429	N	N	N	N
vg0406998246	G -> A	LOC_Os04g12639.1	intron_variant ; MODIFIER	silent_mutation	Average:38.888; most accessible tissue: Callus, score: 65.429	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0406998246	NA	2.15E-14	mr1035	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
vg0406998246	NA	2.33E-13	mr1149	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
vg0406998246	NA	1.04E-06	mr1510	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
vg0406998246	NA	4.56E-06	mr1613	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
vg0406998246	NA	1.18E-13	mr1626	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
vg0406998246	NA	4.87E-07	mr1915	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
vg0406998246	4.07E-06	6.18E-06	mr1062_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
vg0406998246	NA	3.88E-20	mr1095_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
vg0406998246	NA	4.56E-14	mr1097_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
vg0406998246	NA	1.03E-20	mr1146_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
vg0406998246	NA	9.77E-15	mr1148_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
vg0406998246	NA	2.20E-31	mr1150_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
vg0406998246	NA	1.99E-06	mr1153_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
vg0406998246	NA	1.07E-09	mr1222_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
vg0406998246	NA	1.03E-18	mr1239_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
vg0406998246	NA	8.16E-06	mr1525_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
vg0406998246	NA	2.70E-10	mr1835_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
vg0406998246	NA	3.71E-15	mr1936_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