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Detailed information for vg0311641017:

Variant ID: vg0311641017 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 11641017
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.01, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TGTTAGAAAATGCCCCTTTTACCCTACCCTAGAAAAGAGAAAACCAAGATGAATAAACAACAATGCATATGTACTTTCCATTATTTCAACATATACACTT[G/A]
AAACTTGAGTCTAATGGCTATCGTATACACTTGCAAGTACATAATTTAGTTTCGTTTATATAAATTACTATGCACTATCTATAAAAGAATTCATTGCACG

Reverse complement sequence

CGTGCAATGAATTCTTTTATAGATAGTGCATAGTAATTTATATAAACGAAACTAAATTATGTACTTGCAAGTGTATACGATAGCCATTAGACTCAAGTTT[C/T]
AAGTGTATATGTTGAAATAATGGAAAGTACATATGCATTGTTGTTTATTCATCTTGGTTTTCTCTTTTCTAGGGTAGGGTAAAAGGGGCATTTTCTAACA

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	98.80%	0.40%	0.80%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	96.30%	1.20%	2.51%	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	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	92.70%	2.30%	4.95%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0311641017	G -> A	LOC_Os03g20540.1	upstream_gene_variant ; 683.0bp to feature; MODIFIER	silent_mutation	Average:46.471; most accessible tissue: Callus, score: 61.846	N	N	N	N
vg0311641017	G -> A	LOC_Os03g20530-LOC_Os03g20540	intergenic_region ; MODIFIER	silent_mutation	Average:46.471; most accessible tissue: Callus, score: 61.846	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0311641017	4.05E-06	4.05E-06	mr1081_2	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