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Detailed information for vg0400436154:

Variant ID: vg0400436154 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 436154
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, A: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

AGATAAGGAGGAAGGGAAGAAGGGAAGAGATAAGGATTAGAGATGGAGAGAGGAGTTTGTGTGGACGGAAAAAGAGGATAAGTAATAGGGATTATATAGT[G/A]
CGTTTTGATCTTTAATCCCGGTTAGTAACACAAACCGGGACTCCCAGTTTGTGTTATTAACCGGGATTAAAGATCCGATCTTTACTCCCGGTTGGTAACT

Reverse complement sequence

AGTTACCAACCGGGAGTAAAGATCGGATCTTTAATCCCGGTTAATAACACAAACTGGGAGTCCCGGTTTGTGTTACTAACCGGGATTAAAGATCAAAACG[C/T]
ACTATATAATCCCTATTACTTATCCTCTTTTTCCGTCCACACAAACTCCTCTCTCCATCTCTAATCCTTATCTCTTCCCTTCTTCCCTTCCTCCTTATCT

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	73.30%	26.60%	0.04%	0.00%	NA
All Indica	2759	54.80%	45.20%	0.07%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	19.70%	80.30%	0.00%	0.00%	NA
Indica II	465	62.60%	37.40%	0.00%	0.00%	NA
Indica III	913	65.20%	34.80%	0.00%	0.00%	NA
Indica Intermediate	786	64.60%	35.10%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	10.00%	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
vg0400436154	G -> A	LOC_Os04g01640.1	downstream_gene_variant ; 2153.0bp to feature; MODIFIER	silent_mutation	Average:48.191; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N
vg0400436154	G -> A	LOC_Os04g01640-LOC_Os04g01650	intergenic_region ; MODIFIER	silent_mutation	Average:48.191; most accessible tissue: Minghui63 panicle, score: 73.225	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0400436154	NA	5.10E-07	mr1955	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
vg0400436154	1.08E-06	1.08E-06	mr1955	Ind_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