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Detailed information for vg0102103893:

Variant ID: vg0102103893 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 2103893
Reference Allele: G	Alternative Allele: A,T
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

AGTCAGTACGAACTTGGCTCATAAACAGACTAAAATTGTCATACGTTACGTGTATATACGATCAATACATCTAAAATTGTCAGACGTTACGTGTATATAC[G/A,T]
ATCAATACAACGTCATGTCAGCAGTACAACTGGAAATAATACTCAATCAAAAGATCATCATAATAATAAATGTATGCTTAAATACTTAACAACAAGAATG

Reverse complement sequence

CATTCTTGTTGTTAAGTATTTAAGCATACATTTATTATTATGATGATCTTTTGATTGAGTATTATTTCCAGTTGTACTGCTGACATGACGTTGTATTGAT[C/T,A]
GTATATACACGTAACGTCTGACAATTTTAGATGTATTGATCGTATATACACGTAACGTATGACAATTTTAGTCTGTTTATGAGCCAAGTTCGTACTGACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	9.10%	0.08%	0.00%	T: 0.02%
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	74.30%	25.40%	0.20%	0.00%	T: 0.07%
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	74.30%	25.70%	0.00%	0.00%	NA
Tropical Japonica	504	68.80%	30.40%	0.60%	0.00%	T: 0.20%
Japonica Intermediate	241	85.90%	14.10%	0.00%	0.00%	NA
VI/Aromatic	96	63.50%	36.50%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	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
vg0102103893	G -> T	LOC_Os01g04670.1	upstream_gene_variant ; 1221.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> T	LOC_Os01g04680.1	upstream_gene_variant ; 1298.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> T	LOC_Os01g04660.1	downstream_gene_variant ; 3199.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> T	LOC_Os01g04660.2	downstream_gene_variant ; 3199.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> T	LOC_Os01g04670-LOC_Os01g04680	intergenic_region ; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> A	LOC_Os01g04670.1	upstream_gene_variant ; 1221.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> A	LOC_Os01g04680.1	upstream_gene_variant ; 1298.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> A	LOC_Os01g04660.1	downstream_gene_variant ; 3199.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> A	LOC_Os01g04660.2	downstream_gene_variant ; 3199.0bp to feature; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N
vg0102103893	G -> A	LOC_Os01g04670-LOC_Os01g04680	intergenic_region ; MODIFIER	silent_mutation	Average:32.072; most accessible tissue: Zhenshan97 panicle, score: 65.386	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0102103893	2.95E-06	2.95E-06	mr1971_2	Jap_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