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Detailed information for vg0610848809:

Variant ID: vg0610848809 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 10848809
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.64, A: 0.36, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

TAAAAGAAGAAAGAGATCGACTTGGATTTTTATCAAGTTCTAGATCACTAGATTGGATAATAACTCTATTGTCACTGCTACATGTGAGATTTTCCTTGAC[A/G]
CCAGCCCCGCTAGCTTTCAGGCGGGCCGTTTAGTAGCTCCGCCCGGAACAAGCCGAAGGCTGGCGCCGGGGTTAGGGCCGCATGGGATAATGAATTATCT

Reverse complement sequence

AGATAATTCATTATCCCATGCGGCCCTAACCCCGGCGCCAGCCTTCGGCTTGTTCCGGGCGGAGCTACTAAACGGCCCGCCTGAAAGCTAGCGGGGCTGG[T/C]
GTCAAGGAAAATCTCACATGTAGCAGTGACAATAGAGTTATTATCCAATCTAGTGATCTAGAACTTGATAAAAATCCAAGTCGATCTCTTTCTTCTTTTA

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	35.30%	12.90%	2.20%	49.64%	NA
All Indica	2759	6.20%	13.30%	3.26%	77.20%	NA
All Japonica	1512	77.40%	14.60%	0.33%	7.61%	NA
Aus	269	81.80%	1.90%	1.12%	15.24%	NA
Indica I	595	8.40%	3.40%	6.22%	82.02%	NA
Indica II	465	6.00%	1.30%	3.44%	89.25%	NA
Indica III	913	2.00%	24.60%	0.99%	72.40%	NA
Indica Intermediate	786	9.50%	14.90%	3.56%	72.01%	NA
Temperate Japonica	767	70.00%	26.20%	0.39%	3.39%	NA
Tropical Japonica	504	83.30%	2.20%	0.40%	14.09%	NA
Japonica Intermediate	241	88.80%	3.70%	0.00%	7.47%	NA
VI/Aromatic	96	71.90%	8.30%	1.04%	18.75%	NA
Intermediate	90	41.10%	6.70%	5.56%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0610848809	A -> G	LOC_Os06g19070.1	upstream_gene_variant ; 2789.0bp to feature; MODIFIER	silent_mutation	Average:37.029; most accessible tissue: Callus, score: 91.174	N	N	N	N
vg0610848809	A -> G	LOC_Os06g19080.1	upstream_gene_variant ; 1014.0bp to feature; MODIFIER	silent_mutation	Average:37.029; most accessible tissue: Callus, score: 91.174	N	N	N	N
vg0610848809	A -> G	LOC_Os06g19070-LOC_Os06g19080	intergenic_region ; MODIFIER	silent_mutation	Average:37.029; most accessible tissue: Callus, score: 91.174	N	N	N	N
vg0610848809	A -> DEL	N	N	silent_mutation	Average:37.029; most accessible tissue: Callus, score: 91.174	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0610848809	1.38E-06	NA	mr1218	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