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Detailed information for vg0501373128:

Variant ID: vg0501373128 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 1373128
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, A: 0.20, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

TATATTGCTATATTCTGGGACGGAGGGAGTACTAGTTAAAATAAATTTAAAAAATGGATTAATATGGTTTTCTAAAGTAACTTTCATATATAATTTTTTT[T/A]
AAAAAAGTGTACAATTTAATAATTTGAAAAAGATAAAAATGAGGAAGTGTTAACGACCAAATTTGATAAACCATGAATCAGGTTTGGCATTGGAATCAAA

Reverse complement sequence

TTTGATTCCAATGCCAAACCTGATTCATGGTTTATCAAATTTGGTCGTTAACACTTCCTCATTTTTATCTTTTTCAAATTATTAAATTGTACACTTTTTT[A/T]
AAAAAAATTATATATGAAAGTTACTTTAGAAAACCATATTAATCCATTTTTTAAATTTATTTTAACTAGTACTCCCTCCGTCCCAGAATATAGCAATATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	70.30%	29.40%	0.30%	0.00%	NA
All Indica	2759	50.40%	49.10%	0.51%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	98.10%	1.90%	0.00%	0.00%	NA
Indica I	595	27.70%	71.90%	0.34%	0.00%	NA
Indica II	465	38.30%	61.10%	0.65%	0.00%	NA
Indica III	913	75.20%	24.30%	0.44%	0.00%	NA
Indica Intermediate	786	45.80%	53.60%	0.64%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	82.20%	17.80%	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
vg0501373128	T -> A	LOC_Os05g03350.1	upstream_gene_variant ; 2718.0bp to feature; MODIFIER	silent_mutation	Average:11.772; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0501373128	T -> A	LOC_Os05g03360.1	downstream_gene_variant ; 4587.0bp to feature; MODIFIER	silent_mutation	Average:11.772; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N
vg0501373128	T -> A	LOC_Os05g03339-LOC_Os05g03350	intergenic_region ; MODIFIER	silent_mutation	Average:11.772; most accessible tissue: Minghui63 root, score: 21.615	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0501373128	NA	1.81E-06	mr1274	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
vg0501373128	NA	8.75E-06	mr1434	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
vg0501373128	NA	8.90E-08	mr1510	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
vg0501373128	NA	1.58E-06	mr1691	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
vg0501373128	1.18E-07	1.18E-07	mr1779	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
vg0501373128	NA	4.41E-16	mr1807	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
vg0501373128	NA	7.66E-06	mr1807	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