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Detailed information for vg0607519601:

Variant ID: vg0607519601 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7519601
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 123. )

Flanking Sequence (100 bp) in Reference Genome:

AATGAGAGGACATAAATTGGCGTATTAGAGCATCTCCAACAGAATCTCTATTTGACTCTCCAAGTTAAAATTTGGCCAACACAGATAAAAAACGAGCTCC[T/A]
ACAGACTCCCCACCTAGATGCCCAAGCCATCCGGATGGCCAAATTGCTCCACCGGCTGGCCAAATGTAGCCAGCCTCCTCCACTGGCTAAAGGTGGGTCC

Reverse complement sequence

GGACCCACCTTTAGCCAGTGGAGGAGGCTGGCTACATTTGGCCAGCCGGTGGAGCAATTTGGCCATCCGGATGGCTTGGGCATCTAGGTGGGGAGTCTGT[A/T]
GGAGCTCGTTTTTTATCTGTGTTGGCCAAATTTTAACTTGGAGAGTCAAATAGAGATTCTGTTGGAGATGCTCTAATACGCCAATTTATGTCCTCTCATT

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	63.70%	36.10%	0.23%	0.00%	NA
All Indica	2759	38.70%	60.90%	0.40%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	39.70%	60.20%	0.17%	0.00%	NA
Indica II	465	66.50%	33.10%	0.43%	0.00%	NA
Indica III	913	18.40%	81.30%	0.33%	0.00%	NA
Indica Intermediate	786	45.00%	54.30%	0.64%	0.00%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	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
vg0607519601	T -> A	LOC_Os06g13590.1	upstream_gene_variant ; 18.0bp to feature; MODIFIER	silent_mutation	Average:48.833; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0607519601	T -> A	LOC_Os06g13580-LOC_Os06g13590	intergenic_region ; MODIFIER	silent_mutation	Average:48.833; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607519601	NA	4.73E-06	mr1874	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
vg0607519601	NA	4.86E-07	mr1874_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
vg0607519601	NA	1.66E-06	mr1925_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
vg0607519601	1.44E-08	NA	mr1970_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
vg0607519601	2.12E-06	2.56E-08	mr1970_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
vg0607519601	3.59E-10	NA	mr1973_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
vg0607519601	1.21E-08	1.69E-08	mr1973_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