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Detailed information for vg1102558247:

Variant ID: vg1102558247 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 2558247
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.97, A: 0.02, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

GTGGTGTTTGGATCCATAAGTCCTAGGGACTTATTTCAGTCCTAAGACTAATCACTTTAGTCCATGGTTGTTTTGTTATAGGGACTAAAGTTCATTAAAT[G/A]
CGCTGCACAATAACCATGTTGTCTCTAAAACCATGCAAAGAGAAATACACCATGTCCATGCATGAGGGCAGCAAGTGGAAAAAAGCTACTTTAGTACCAA

Reverse complement sequence

TTGGTACTAAAGTAGCTTTTTTCCACTTGCTGCCCTCATGCATGGACATGGTGTATTTCTCTTTGCATGGTTTTAGAGACAACATGGTTATTGTGCAGCG[C/T]
ATTTAATGAACTTTAGTCCCTATAACAAAACAACCATGGACTAAAGTGATTAGTCTTAGGACTGAAATAAGTCCCTAGGACTTATGGATCCAAACACCAC

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	80.10%	12.30%	0.91%	6.75%	NA
All Indica	2759	71.20%	18.60%	0.65%	9.60%	NA
All Japonica	1512	91.60%	4.00%	1.26%	3.17%	NA
Aus	269	97.80%	0.00%	1.12%	1.12%	NA
Indica I	595	72.10%	16.10%	0.67%	11.09%	NA
Indica II	465	85.20%	6.00%	1.29%	7.53%	NA
Indica III	913	62.90%	29.40%	0.22%	7.56%	NA
Indica Intermediate	786	71.90%	15.30%	0.76%	12.09%	NA
Temperate Japonica	767	90.60%	7.40%	1.69%	0.26%	NA
Tropical Japonica	504	89.90%	0.40%	0.79%	8.93%	NA
Japonica Intermediate	241	98.30%	0.40%	0.83%	0.41%	NA
VI/Aromatic	96	95.80%	0.00%	2.08%	2.08%	NA
Intermediate	90	88.90%	8.90%	1.11%	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
vg1102558247	G -> A	LOC_Os11g05630.1	upstream_gene_variant ; 3471.0bp to feature; MODIFIER	silent_mutation	Average:39.503; most accessible tissue: Callus, score: 91.338	N	N	N	N
vg1102558247	G -> A	LOC_Os11g05640.1	upstream_gene_variant ; 2569.0bp to feature; MODIFIER	silent_mutation	Average:39.503; most accessible tissue: Callus, score: 91.338	N	N	N	N
vg1102558247	G -> A	LOC_Os11g05630-LOC_Os11g05640	intergenic_region ; MODIFIER	silent_mutation	Average:39.503; most accessible tissue: Callus, score: 91.338	N	N	N	N
vg1102558247	G -> DEL	N	N	silent_mutation	Average:39.503; most accessible tissue: Callus, score: 91.338	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1102558247	7.75E-09	2.41E-10	mr1588_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