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Detailed information for vg0332706732:

Variant ID: vg0332706732 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 32706732
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGTTTAACTATGTACTGTACTAAGTTAAGAGCCTCATTGGTTGCCTTAATAAGTCAAAGCCAAAACTAAAATTTAAATTTCCAAACTTAATTTTAAAATT[G/A]
ATTTTAAGATATTTTCAACTTAGTTTCTTTTATAGTGTTATTTAACTTTTAAGTCAATAAGAGCACATATATAAAAGTTTTACCTAAAAACTAATTTTTA

Reverse complement sequence

TAAAAATTAGTTTTTAGGTAAAACTTTTATATATGTGCTCTTATTGACTTAAAAGTTAAATAACACTATAAAAGAAACTAAGTTGAAAATATCTTAAAAT[C/T]
AATTTTAAAATTAAGTTTGGAAATTTAAATTTTAGTTTTGGCTTTGACTTATTAAGGCAACCAATGAGGCTCTTAACTTAGTACAGTACATAGTTAAACC

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	97.80%	2.00%	0.19%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	93.50%	6.00%	0.60%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	81.50%	16.90%	1.59%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0332706732	G -> A	LOC_Os03g57330.1	upstream_gene_variant ; 2233.0bp to feature; MODIFIER	silent_mutation	Average:47.346; most accessible tissue: Callus, score: 85.692	N	N	N	N
vg0332706732	G -> A	LOC_Os03g57340.1	upstream_gene_variant ; 1679.0bp to feature; MODIFIER	silent_mutation	Average:47.346; most accessible tissue: Callus, score: 85.692	N	N	N	N
vg0332706732	G -> A	LOC_Os03g57330.3	upstream_gene_variant ; 2359.0bp to feature; MODIFIER	silent_mutation	Average:47.346; most accessible tissue: Callus, score: 85.692	N	N	N	N
vg0332706732	G -> A	LOC_Os03g57330-LOC_Os03g57340	intergenic_region ; MODIFIER	silent_mutation	Average:47.346; most accessible tissue: Callus, score: 85.692	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0332706732	6.21E-07	6.83E-07	mr1871	Jap_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