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Detailed information for vg0332638761:

Variant ID: vg0332638761 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32638761
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

AGTTAGACCCCAATTCTTTTTTAGTCCCAGTTGGTATAAACAACAGGACTCCCGATTGTTTATACCAACCAGGACAAAAAAAAAATCAACCGAGCTGGCG[C/A]
CACTGCCCCGCCCGGCCGCCTCGGTCTCTCCCCCTTCCTTTCCCCTCCCCTCTCATTAATTAAATAGCCTCATCCATCCCTTCTCCATCCTTATCCTCCT

Reverse complement sequence

AGGAGGATAAGGATGGAGAAGGGATGGATGAGGCTATTTAATTAATGAGAGGGGAGGGGAAAGGAAGGGGGAGAGACCGAGGCGGCCGGGCGGGGCAGTG[G/T]
CGCCAGCTCGGTTGATTTTTTTTTTGTCCTGGTTGGTATAAACAATCGGGAGTCCTGTTGTTTATACCAACTGGGACTAAAAAAGAATTGGGGTCTAACT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.60%	12.10%	0.30%	0.00%	NA
All Indica	2759	79.50%	20.00%	0.47%	0.00%	NA
All Japonica	1512	99.60%	0.40%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.60%	9.10%	0.34%	0.00%	NA
Indica II	465	74.40%	24.70%	0.86%	0.00%	NA
Indica III	913	79.80%	20.20%	0.00%	0.00%	NA
Indica Intermediate	786	73.80%	25.30%	0.89%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	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	81.10%	17.80%	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
vg0332638761	C -> A	LOC_Os03g57230-LOC_Os03g57240	intergenic_region ; MODIFIER	silent_mutation	Average:56.183; most accessible tissue: Minghui63 panicle, score: 77.956	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332638761	4.12E-06	4.31E-06	mr1673	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