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Detailed information for vg1204159174:

Variant ID: vg1204159174 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 4159174
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATTCTTTTTCCTTCAGTGGTAGATCCAGCTTTCTCGTGGACACACTCATTTTTTTTAGACACCCACAGACTTAACCATGTTACCATGTACTACCTCT[A/G]
TATTTTAATGTATGACGTTATTGACTTTTTGTCCAACGTTTGACCATTCGTCTTATTCAAAAAATTTATGTAATTATTATTTATTTTATTGTGACTTGAT

Reverse complement sequence

ATCAAGTCACAATAAAATAAATAATAATTACATAAATTTTTTGAATAAGACGAATGGTCAAACGTTGGACAAAAAGTCAATAACGTCATACATTAAAATA[T/C]
AGAGGTAGTACATGGTAACATGGTTAAGTCTGTGGGTGTCTAAAAAAAATGAGTGTGTCCACGAGAAAGCTGGATCTACCACTGAAGGAAAAAGAATTAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	35.50%	1.20%	2.24%	60.96%	NA
All Indica	2759	4.80%	2.00%	3.70%	89.45%	NA
All Japonica	1512	86.30%	0.00%	0.07%	13.62%	NA
Aus	269	39.00%	0.70%	0.00%	60.22%	NA
Indica I	595	1.70%	4.90%	7.39%	86.05%	NA
Indica II	465	4.10%	0.90%	2.15%	92.90%	NA
Indica III	913	5.10%	0.70%	2.52%	91.68%	NA
Indica Intermediate	786	7.30%	2.20%	3.18%	87.40%	NA
Temperate Japonica	767	93.40%	0.00%	0.00%	6.65%	NA
Tropical Japonica	504	85.50%	0.00%	0.00%	14.48%	NA
Japonica Intermediate	241	65.60%	0.00%	0.41%	34.02%	NA
VI/Aromatic	96	84.40%	0.00%	0.00%	15.62%	NA
Intermediate	90	62.20%	1.10%	3.33%	33.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1204159174	A -> DEL	N	N	silent_mutation	Average:49.846; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N
vg1204159174	A -> G	LOC_Os12g08140.1	upstream_gene_variant ; 4459.0bp to feature; MODIFIER	silent_mutation	Average:49.846; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N
vg1204159174	A -> G	LOC_Os12g08130-LOC_Os12g08140	intergenic_region ; MODIFIER	silent_mutation	Average:49.846; most accessible tissue: Zhenshan97 root, score: 75.661	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1204159174	9.96E-07	6.18E-13	mr1457	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
vg1204159174	2.23E-06	9.43E-08	mr1457	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