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Detailed information for vg1124181870:

Variant ID: vg1124181870 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 24181870
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 101. )

Flanking Sequence (100 bp) in Reference Genome:

AAATACACCGAGTAGCGGTTTAGGAAGCATGCTAAAAATAAACAAGAAAAAAGCCAAACACAAAATCTGATAAGAAGACACCATTTAACCGTCATCGCAC[A/G]
AAACAATGTTTATTATAGAGGAAAACACAACACAGTTATTTTTGGATGGTAATTAATTGTCTGCTTTCTTTTTTTCTTTCAAATTTCAAAAATTAATTGT

Reverse complement sequence

ACAATTAATTTTTGAAATTTGAAAGAAAAAAAGAAAGCAGACAATTAATTACCATCCAAAAATAACTGTGTTGTGTTTTCCTCTATAATAAACATTGTTT[T/C]
GTGCGATGACGGTTAAATGGTGTCTTCTTATCAGATTTTGTGTTTGGCTTTTTTCTTGTTTATTTTTAGCATGCTTCCTAAACCGCTACTCGGTGTATTT

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	69.70%	28.70%	1.65%	0.00%	NA
All Indica	2759	83.00%	16.50%	0.51%	0.00%	NA
All Japonica	1512	57.00%	39.10%	3.90%	0.00%	NA
Aus	269	26.00%	74.00%	0.00%	0.00%	NA
Indica I	595	89.10%	9.40%	1.51%	0.00%	NA
Indica II	465	93.30%	6.20%	0.43%	0.00%	NA
Indica III	913	73.30%	26.60%	0.11%	0.00%	NA
Indica Intermediate	786	83.50%	16.30%	0.25%	0.00%	NA
Temperate Japonica	767	60.40%	32.50%	7.17%	0.00%	NA
Tropical Japonica	504	45.60%	54.20%	0.20%	0.00%	NA
Japonica Intermediate	241	70.10%	28.60%	1.24%	0.00%	NA
VI/Aromatic	96	17.70%	82.30%	0.00%	0.00%	NA
Intermediate	90	62.20%	32.20%	5.56%	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
vg1124181870	A -> G	LOC_Os11g40540.1	upstream_gene_variant ; 2740.0bp to feature; MODIFIER	silent_mutation	Average:19.971; most accessible tissue: Callus, score: 47.616	N	N	N	N
vg1124181870	A -> G	LOC_Os11g40540.2	upstream_gene_variant ; 2740.0bp to feature; MODIFIER	silent_mutation	Average:19.971; most accessible tissue: Callus, score: 47.616	N	N	N	N
vg1124181870	A -> G	LOC_Os11g40520.1	downstream_gene_variant ; 2620.0bp to feature; MODIFIER	silent_mutation	Average:19.971; most accessible tissue: Callus, score: 47.616	N	N	N	N
vg1124181870	A -> G	LOC_Os11g40530.1	downstream_gene_variant ; 436.0bp to feature; MODIFIER	silent_mutation	Average:19.971; most accessible tissue: Callus, score: 47.616	N	N	N	N
vg1124181870	A -> G	LOC_Os11g40530-LOC_Os11g40540	intergenic_region ; MODIFIER	silent_mutation	Average:19.971; most accessible tissue: Callus, score: 47.616	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1124181870	NA	6.61E-06	mr1693_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