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Detailed information for vg0114839906:

Variant ID: vg0114839906 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14839906
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTCTCTGTTTCAGTAGTCTTTAGCCTGTTTGTATTGTTTGCTTTGTATGTCGCTTAGATTCCGGCTCTCCTGACGCTCCGGTGTACTTTGAAATAGTC[A/G]
CCGAGGTTCCTCCAGCAGTAGAGCAAGGCAAGTCATGCTTGTCACTTGAACATGTTGATCCTATATTGCAAATGCTCTATCGTTTTCCTTTAAATACTGC

Reverse complement sequence

GCAGTATTTAAAGGAAAACGATAGAGCATTTGCAATATAGGATCAACATGTTCAAGTGACAAGCATGACTTGCCTTGCTCTACTGCTGGAGGAACCTCGG[T/C]
GACTATTTCAAAGTACACCGGAGCGTCAGGAGAGCCGGAATCTAAGCGACATACAAAGCAAACAATACAAACAGGCTAAAGACTACTGAAACAGAGAACA

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	32.90%	8.40%	1.95%	56.71%	NA
All Indica	2759	3.20%	14.00%	3.04%	79.74%	NA
All Japonica	1512	86.10%	0.00%	0.13%	13.76%	NA
Aus	269	30.90%	1.90%	1.86%	65.43%	NA
Indica I	595	2.70%	23.90%	6.05%	67.39%	NA
Indica II	465	4.90%	19.10%	2.80%	73.12%	NA
Indica III	913	2.00%	4.30%	0.66%	93.10%	NA
Indica Intermediate	786	3.90%	14.90%	3.69%	77.48%	NA
Temperate Japonica	767	93.70%	0.00%	0.00%	6.26%	NA
Tropical Japonica	504	89.70%	0.00%	0.20%	10.12%	NA
Japonica Intermediate	241	54.40%	0.00%	0.41%	45.23%	NA
VI/Aromatic	96	38.50%	0.00%	0.00%	61.46%	NA
Intermediate	90	50.00%	7.80%	1.11%	41.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114839906	A -> G	LOC_Os01g26190.1	downstream_gene_variant ; 1249.0bp to feature; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0114839906	A -> G	LOC_Os01g26174-LOC_Os01g26190	intergenic_region ; MODIFIER	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0114839906	A -> DEL	N	N	silent_mutation	Average:6.317; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114839906	3.38E-06	3.27E-06	mr1642	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
vg0114839906	1.95E-06	1.98E-06	mr1684	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
vg0114839906	NA	4.89E-07	mr1785	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