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Detailed information for vg0320942236:

Variant ID: vg0320942236 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 20942236
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: 120. )

Flanking Sequence (100 bp) in Reference Genome:

TTACATATGTAATTTTAGTTATATAAGACTGTAATTTTATATTTTAAAGAAAATAATAAGTACATATTTACTTACACATTATTTTTATCAAAATTACAGT[G/A]
CACTTACATGTAAATCAACTAAATTTACAAATGTAATTTTAGTTATATAGGACTGTAATTTTATATTTTAAAGAAAATAATAAGTACATATTTACTAACA

Reverse complement sequence

TGTTAGTAAATATGTACTTATTATTTTCTTTAAAATATAAAATTACAGTCCTATATAACTAAAATTACATTTGTAAATTTAGTTGATTTACATGTAAGTG[C/T]
ACTGTAATTTTGATAAAAATAATGTGTAAGTAAATATGTACTTATTATTTTCTTTAAAATATAAAATTACAGTCTTATATAACTAAAATTACATATGTAA

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	41.70%	7.80%	18.54%	31.95%	NA
All Indica	2759	28.30%	12.60%	12.79%	46.21%	NA
All Japonica	1512	57.00%	0.10%	32.47%	10.38%	NA
Aus	269	79.20%	4.80%	1.86%	14.13%	NA
Indica I	595	44.20%	4.70%	9.24%	41.85%	NA
Indica II	465	21.70%	9.00%	15.91%	53.33%	NA
Indica III	913	25.20%	20.20%	11.28%	43.37%	NA
Indica Intermediate	786	23.90%	12.10%	15.39%	48.60%	NA
Temperate Japonica	767	44.70%	0.10%	42.63%	12.52%	NA
Tropical Japonica	504	73.60%	0.20%	19.05%	7.14%	NA
Japonica Intermediate	241	61.40%	0.00%	28.22%	10.37%	NA
VI/Aromatic	96	81.20%	0.00%	9.38%	9.38%	NA
Intermediate	90	40.00%	5.60%	20.00%	34.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0320942236	G -> A	LOC_Os03g37760.1	downstream_gene_variant ; 4669.0bp to feature; MODIFIER	silent_mutation	Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0320942236	G -> A	LOC_Os03g37770.1	downstream_gene_variant ; 1780.0bp to feature; MODIFIER	silent_mutation	Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0320942236	G -> A	LOC_Os03g37780.1	downstream_gene_variant ; 2792.0bp to feature; MODIFIER	silent_mutation	Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0320942236	G -> A	LOC_Os03g37770-LOC_Os03g37780	intergenic_region ; MODIFIER	silent_mutation	Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0320942236	G -> DEL	N	N	silent_mutation	Average:9.441; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0320942236	7.89E-06	7.88E-06	mr1494	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
vg0320942236	3.56E-06	3.56E-06	mr1494	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
vg0320942236	NA	1.02E-07	mr1785	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