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Detailed information for vg1119346406:

Variant ID: vg1119346406 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 19346406
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.91, A: 0.08, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

GATCTACATCGGTCAGACCGACGTGTTCCAGGCGGTCAGACCGGCGCATCTACTTCAGTCAGACCGCAATCCGTCGAATTTGAGGGTAACTTTTATTTCC[G/A]
CTAAAAGTTTCAGTTTTTGGGTATACCAACCATTCACCCCATTTGATTGGCTTAGTTGTTGTGATTCGATCCTATAAAGATAGGTAAAACGGAGTGAGTC

Reverse complement sequence

GACTCACTCCGTTTTACCTATCTTTATAGGATCGAATCACAACAACTAAGCCAATCAAATGGGGTGAATGGTTGGTATACCCAAAAACTGAAACTTTTAG[C/T]
GGAAATAAAAGTTACCCTCAAATTCGACGGATTGCGGTCTGACTGAAGTAGATGCGCCGGTCTGACCGCCTGGAACACGTCGGTCTGACCGATGTAGATC

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	93.50%	6.50%	0.00%	0.00%	NA
All Indica	2759	95.50%	4.50%	0.00%	0.00%	NA
All Japonica	1512	95.00%	5.00%	0.00%	0.00%	NA
Aus	269	61.30%	38.70%	0.00%	0.00%	NA
Indica I	595	98.50%	1.50%	0.00%	0.00%	NA
Indica II	465	91.20%	8.80%	0.00%	0.00%	NA
Indica III	913	97.80%	2.20%	0.00%	0.00%	NA
Indica Intermediate	786	93.00%	7.00%	0.00%	0.00%	NA
Temperate Japonica	767	97.50%	2.50%	0.00%	0.00%	NA
Tropical Japonica	504	92.70%	7.30%	0.00%	0.00%	NA
Japonica Intermediate	241	92.10%	7.90%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg1119346406	G -> A	LOC_Os11g32740.1	upstream_gene_variant ; 2594.0bp to feature; MODIFIER	silent_mutation	Average:51.888; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N
vg1119346406	G -> A	LOC_Os11g32720-LOC_Os11g32740	intergenic_region ; MODIFIER	silent_mutation	Average:51.888; most accessible tissue: Minghui63 root, score: 68.289	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1119346406	6.96E-06	NA	mr1187_2	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
vg1119346406	NA	1.89E-07	mr1354_2	Ind_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