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Detailed information for vg0431921919:

Variant ID: vg0431921919 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 31921919
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

GATTTATATTGTCTCGGCATGGCGACCGATCTATTCCAATCACTTGATTTAAGTATATATCGATACAAAGATTATATATTGTCAATATCTGCAGCCGATC[G/A]
AGTAGATCTAGTCCCTTCTTATTTATTAATGACTGCCGATCGATGTATATATGACATCGGCTCAAAGATAAATGATATGTCATCGGCACCTAGCCGATCG

Reverse complement sequence

CGATCGGCTAGGTGCCGATGACATATCATTTATCTTTGAGCCGATGTCATATATACATCGATCGGCAGTCATTAATAAATAAGAAGGGACTAGATCTACT[C/T]
GATCGGCTGCAGATATTGACAATATATAATCTTTGTATCGATATATACTTAAATCAAGTGATTGGAATAGATCGGTCGCCATGCCGAGACAATATAAATC

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	72.30%	27.30%	0.38%	0.00%	NA
All Indica	2759	55.80%	43.70%	0.51%	0.00%	NA
All Japonica	1512	97.90%	2.00%	0.13%	0.00%	NA
Aus	269	86.20%	13.80%	0.00%	0.00%	NA
Indica I	595	38.80%	61.00%	0.17%	0.00%	NA
Indica II	465	75.10%	24.90%	0.00%	0.00%	NA
Indica III	913	55.90%	43.80%	0.33%	0.00%	NA
Indica Intermediate	786	57.10%	41.60%	1.27%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	95.20%	4.80%	0.00%	0.00%	NA
Japonica Intermediate	241	97.50%	2.10%	0.41%	0.00%	NA
VI/Aromatic	96	96.90%	2.10%	1.04%	0.00%	NA
Intermediate	90	80.00%	18.90%	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
vg0431921919	G -> A	LOC_Os04g53550.1	downstream_gene_variant ; 3736.0bp to feature; MODIFIER	silent_mutation	Average:25.337; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N
vg0431921919	G -> A	LOC_Os04g53544-LOC_Os04g53550	intergenic_region ; MODIFIER	silent_mutation	Average:25.337; most accessible tissue: Zhenshan97 panicle, score: 46.362	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0431921919	2.25E-06	NA	mr1189_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
vg0431921919	NA	8.48E-07	mr1265_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