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Detailed information for vg0607527077:

Variant ID: vg0607527077 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 7527077
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.62, G: 0.38, others allele: 0.00, population size: 105. )

Flanking Sequence (100 bp) in Reference Genome:

AATTAGTATGAGTGATAGTTTATTCAACATGCCTTCCTCTCAATCACTAGTCTAGCTAGCTAATCTGTCATCTACTGTACTTTCTAAATTGCTAGCTATA[G/T]
CTATTTATATAGATTTTAGAGTCATGTGCGCTGTGTCATATATATATTTCTTATTTTGTTAGCTAAAAGTTGGTATGGGTTCAAATATGAGAAAATCTAT

Reverse complement sequence

ATAGATTTTCTCATATTTGAACCCATACCAACTTTTAGCTAACAAAATAAGAAATATATATATGACACAGCGCACATGACTCTAAAATCTATATAAATAG[C/A]
TATAGCTAGCAATTTAGAAAGTACAGTAGATGACAGATTAGCTAGCTAGACTAGTGATTGAGAGGAAGGCATGTTGAATAAACTATCACTCATACTAATT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	60.80%	39.20%	0.02%	0.00%	NA
All Indica	2759	36.80%	63.20%	0.04%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	99.30%	0.70%	0.00%	0.00%	NA
Indica I	595	33.60%	66.20%	0.17%	0.00%	NA
Indica II	465	66.20%	33.80%	0.00%	0.00%	NA
Indica III	913	18.10%	81.90%	0.00%	0.00%	NA
Indica Intermediate	786	43.40%	56.60%	0.00%	0.00%	NA
Temperate Japonica	767	99.30%	0.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	24.00%	76.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	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
vg0607527077	G -> T	LOC_Os06g13600.1	upstream_gene_variant ; 3757.0bp to feature; MODIFIER	silent_mutation	Average:36.209; most accessible tissue: Callus, score: 86.201	N	N	N	N
vg0607527077	G -> T	LOC_Os06g13590-LOC_Os06g13600	intergenic_region ; MODIFIER	silent_mutation	Average:36.209; most accessible tissue: Callus, score: 86.201	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0607527077	NA	2.82E-06	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
vg0607527077	7.05E-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
vg0607527077	4.08E-07	1.33E-08	mr1970_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
vg0607527077	9.46E-09	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
vg0607527077	1.96E-07	2.07E-08	mr1973_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