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Detailed information for vg0308100534:

Variant ID: vg0308100534 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 8100534
Reference Allele: A	Alternative Allele: C
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, A: 0.00, others allele: 0.00, population size: 291. )

Flanking Sequence (100 bp) in Reference Genome:

ATGATAGAAGCTCATTTTAAAATAAGTGTAAAGAGAGTCAGCCTAATAGGCAGGTGAGTATAATACTGTGGCCCAACTATTGTGGTCATGCGTGTCCTTG[A/C]
AGTGAAATTAGTACCATAATGGTATGGCTGTGAAGCACTCCACATGTGTATGCGACCGACATGGGGTATTATGATCTACAAAGTTTGGATCCCACGGTGT

Reverse complement sequence

ACACCGTGGGATCCAAACTTTGTAGATCATAATACCCCATGTCGGTCGCATACACATGTGGAGTGCTTCACAGCCATACCATTATGGTACTAATTTCACT[T/G]
CAAGGACACGCATGACCACAATAGTTGGGCCACAGTATTATACTCACCTGCCTATTAGGCTGACTCTCTTTACACTTATTTTAAAATGAGCTTCTATCAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	79.40%	20.40%	0.04%	0.19%	NA
All Indica	2759	99.30%	0.40%	0.04%	0.18%	NA
All Japonica	1512	39.70%	60.10%	0.07%	0.20%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.00%	0.17%	NA
Indica II	465	99.60%	0.20%	0.00%	0.22%	NA
Indica III	913	99.30%	0.50%	0.00%	0.11%	NA
Indica Intermediate	786	98.90%	0.80%	0.13%	0.25%	NA
Temperate Japonica	767	31.20%	68.60%	0.13%	0.13%	NA
Tropical Japonica	504	35.90%	63.70%	0.00%	0.40%	NA
Japonica Intermediate	241	74.70%	25.30%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	16.70%	0.00%	0.00%	NA
Intermediate	90	70.00%	28.90%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0308100534	A -> C	LOC_Os03g14850.1	upstream_gene_variant ; 1770.0bp to feature; MODIFIER	silent_mutation	Average:66.835; most accessible tissue: Callus, score: 87.218	N	N	N	N
vg0308100534	A -> C	LOC_Os03g14860.1	downstream_gene_variant ; 1038.0bp to feature; MODIFIER	silent_mutation	Average:66.835; most accessible tissue: Callus, score: 87.218	N	N	N	N
vg0308100534	A -> C	LOC_Os03g14850-LOC_Os03g14860	intergenic_region ; MODIFIER	silent_mutation	Average:66.835; most accessible tissue: Callus, score: 87.218	N	N	N	N
vg0308100534	A -> DEL	N	N	silent_mutation	Average:66.835; most accessible tissue: Callus, score: 87.218	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0308100534	4.34E-07	NA	mr1712	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
vg0308100534	NA	8.70E-09	mr1020_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
vg0308100534	NA	9.73E-07	mr1355_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