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Detailed information for vg0604988139:

Variant ID: vg0604988139 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 4988139
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.93, G: 0.06, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CGATTAAGTTTATAGAAAAATATAGTAGTATTTTCAACCCAAAACAAATATATTATTAAAATATATTCAATCTTAGATTTAATAAAACTAATTTGATATT[T/G]
TATATGTTTTTAATTTTTGCTATAAATTTAACCAGGAAAAAAGTCAAACGATTTATAATATGGAACGGAGGAAGTATATATGATATGAAATTTATGGTAC

Reverse complement sequence

GTACCATAAATTTCATATCATATATACTTCCTCCGTTCCATATTATAAATCGTTTGACTTTTTTCCTGGTTAAATTTATAGCAAAAATTAAAAACATATA[A/C]
AATATCAAATTAGTTTTATTAAATCTAAGATTGAATATATTTTAATAATATATTTGTTTTGGGTTGAAAATACTACTATATTTTTCTATAAACTTAATCG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	56.00%	43.90%	0.15%	0.00%	NA
All Indica	2759	36.90%	63.00%	0.11%	0.00%	NA
All Japonica	1512	85.50%	14.40%	0.13%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	44.40%	55.10%	0.50%	0.00%	NA
Indica II	465	36.30%	63.70%	0.00%	0.00%	NA
Indica III	913	32.40%	67.60%	0.00%	0.00%	NA
Indica Intermediate	786	36.90%	63.10%	0.00%	0.00%	NA
Temperate Japonica	767	85.80%	14.00%	0.26%	0.00%	NA
Tropical Japonica	504	87.90%	12.10%	0.00%	0.00%	NA
Japonica Intermediate	241	79.70%	20.30%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	62.20%	35.60%	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
vg0604988139	T -> G	LOC_Os06g09790.1	upstream_gene_variant ; 3080.0bp to feature; MODIFIER	silent_mutation	Average:19.359; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0604988139	T -> G	LOC_Os06g09780-LOC_Os06g09790	intergenic_region ; MODIFIER	silent_mutation	Average:19.359; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0604988139	NA	2.43E-06	mr1201	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
vg0604988139	5.73E-06	4.87E-13	mr1201	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
vg0604988139	NA	5.25E-07	mr1219	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
vg0604988139	NA	5.16E-12	mr1219	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
vg0604988139	9.95E-07	5.91E-07	mr1274	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
vg0604988139	4.57E-07	7.58E-13	mr1274	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
vg0604988139	NA	9.21E-06	mr1170_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
vg0604988139	1.57E-06	4.58E-08	mr1201_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
vg0604988139	4.70E-08	2.36E-14	mr1201_2	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
vg0604988139	NA	2.09E-07	mr1219_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
vg0604988139	1.41E-06	9.48E-12	mr1219_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
vg0604988139	3.54E-08	2.59E-09	mr1274_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
vg0604988139	9.90E-07	3.40E-13	mr1274_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