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Detailed information for vg0225321246:

Variant ID: vg0225321246 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 25321246
Reference Allele: T	Alternative Allele: C,G
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, C: 0.02, others allele: 0.00, population size: 277. )

Flanking Sequence (100 bp) in Reference Genome:

AAGAAATTGATGATATCGCTTCAATTGCACAAGCATGCTTGAAAGCTAAAGGAGGAGAGAGACCTACTATGAAAGAAGTAGAAATGAGATTGCAGTTTCT[T/C,G]
AGAACTACCAGACTAAAAAAGTGCCAACCCATTTCTGTAATGGATGAAGAGATTGAGCCTTTTATTTGTCCAAAGACCATTAGCTCTGATGCTCAAAGCA

Reverse complement sequence

TGCTTTGAGCATCAGAGCTAATGGTCTTTGGACAAATAAAAGGCTCAATCTCTTCATCCATTACAGAAATGGGTTGGCACTTTTTTAGTCTGGTAGTTCT[A/G,C]
AGAAACTGCAATCTCATTTCTACTTCTTTCATAGTAGGTCTCTCTCCTCCTTTAGCTTTCAAGCATGCTTGTGCAATTGAAGCGATATCATCAATTTCTT

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	62.90%	36.80%	0.32%	0.00%	NA
All Indica	2759	44.50%	55.10%	0.40%	0.00%	NA
All Japonica	1512	95.70%	4.10%	0.20%	0.00%	NA
Aus	269	63.60%	36.40%	0.00%	0.00%	NA
Indica I	595	25.70%	73.60%	0.67%	0.00%	NA
Indica II	465	50.50%	49.20%	0.22%	0.00%	NA
Indica III	913	51.30%	48.50%	0.22%	0.00%	NA
Indica Intermediate	786	47.20%	52.30%	0.51%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	88.90%	10.90%	0.20%	0.00%	NA
Japonica Intermediate	241	97.50%	1.70%	0.83%	0.00%	NA
VI/Aromatic	96	69.80%	30.20%	0.00%	0.00%	NA
Intermediate	90	66.70%	32.20%	1.11%	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
vg0225321246	T -> G	LOC_Os02g42110.1	synonymous_variant ; p.Leu684Leu; LOW	N	Average:44.467; most accessible tissue: Callus, score: 75.079	N	N	N	N
vg0225321246	T -> G	LOC_Os02g42120.1	upstream_gene_variant ; 1679.0bp to feature; MODIFIER	N	Average:44.467; most accessible tissue: Callus, score: 75.079	N	N	N	N
vg0225321246	T -> C	LOC_Os02g42110.1	synonymous_variant ; p.Leu684Leu; LOW	synonymous_codon	Average:44.467; most accessible tissue: Callus, score: 75.079	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0225321246	NA	8.00E-07	mr1389	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
vg0225321246	8.47E-06	8.47E-06	mr1883	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
vg0225321246	NA	3.55E-06	mr1042_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
vg0225321246	NA	1.17E-07	mr1291_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
vg0225321246	NA	1.88E-10	mr1457_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
vg0225321246	NA	3.11E-09	mr1458_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
vg0225321246	NA	9.41E-06	mr1479_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
vg0225321246	NA	1.95E-06	mr1543_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
vg0225321246	NA	4.23E-08	mr1892_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