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Detailed information for vg0708973974:

Variant ID: vg0708973974 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 8973974
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGTTTGAGCACTTTAGATACCTTGTGGGCTGTCACTTGGGCTTATTACTCTTGGAGATCTTCTCCTAGACGGTTAGGTGTCGCCCGTGAGCTTCCAAA[G/T]
ATCTTGTGGATGTCCCGGGAAAGTTTGTGAAGGTTTTTCTCACCTCCGCAAGGAAATGAGGTAAGTGAGTAAAGATTCTTGTGCTGAGTTTTCAGAGGTT

Reverse complement sequence

AACCTCTGAAAACTCAGCACAAGAATCTTTACTCACTTACCTCATTTCCTTGCGGAGGTGAGAAAAACCTTCACAAACTTTCCCGGGACATCCACAAGAT[C/A]
TTTGGAAGCTCACGGGCGACACCTAACCGTCTAGGAGAAGATCTCCAAGAGTAATAAGCCCAAGTGACAGCCCACAAGGTATCTAAAGTGCTCAAACAAA

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	62.00%	37.10%	0.87%	0.02%	NA
All Indica	2759	37.70%	60.90%	1.34%	0.04%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	88.10%	11.20%	0.74%	0.00%	NA
Indica I	595	81.20%	18.50%	0.34%	0.00%	NA
Indica II	465	15.10%	84.30%	0.65%	0.00%	NA
Indica III	913	12.60%	85.00%	2.30%	0.11%	NA
Indica Intermediate	786	47.30%	51.30%	1.40%	0.00%	NA
Temperate Japonica	767	99.20%	0.70%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	63.30%	35.60%	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
vg0708973974	G -> DEL	N	N	silent_mutation	Average:17.645; most accessible tissue: Zhenshan97 flower, score: 25.055	N	N	N	N
vg0708973974	G -> T	LOC_Os07g15470.1	upstream_gene_variant ; 692.0bp to feature; MODIFIER	silent_mutation	Average:17.645; most accessible tissue: Zhenshan97 flower, score: 25.055	N	N	N	N
vg0708973974	G -> T	LOC_Os07g15460.1	downstream_gene_variant ; 3092.0bp to feature; MODIFIER	silent_mutation	Average:17.645; most accessible tissue: Zhenshan97 flower, score: 25.055	N	N	N	N
vg0708973974	G -> T	LOC_Os07g15460.2	downstream_gene_variant ; 3092.0bp to feature; MODIFIER	silent_mutation	Average:17.645; most accessible tissue: Zhenshan97 flower, score: 25.055	N	N	N	N
vg0708973974	G -> T	LOC_Os07g15460-LOC_Os07g15470	intergenic_region ; MODIFIER	silent_mutation	Average:17.645; most accessible tissue: Zhenshan97 flower, score: 25.055	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0708973974	6.03E-06	NA	mr1888	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
vg0708973974	1.54E-06	NA	mr1888	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