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Detailed information for vg0314845815:

Variant ID: vg0314845815 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14845815
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

GTCCATATGTATAAATTCATAAACCAAATGAACTGAAGTGGAAATTTTAGCAAAATTAGGTCACTAAACTGAGTACTGATTTATGTTCAAGCACCTCCAC[A/G]
GACAAAATTGAAAAAGGAACAGCCATGTTTGATCAAGGTAAACAACAAGTCCTTAAGGGGTGATACCCAAAGAAAAATACTGGTTAACTCATATTTGGTT

Reverse complement sequence

AACCAAATATGAGTTAACCAGTATTTTTCTTTGGGTATCACCCCTTAAGGACTTGTTGTTTACCTTGATCAAACATGGCTGTTCCTTTTTCAATTTTGTC[T/C]
GTGGAGGTGCTTGAACATAAATCAGTACTCAGTTTAGTGACCTAATTTTGCTAAAATTTCCACTTCAGTTCATTTGGTTTATGAATTTATACATATGGAC

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.90%	7.90%	1.25%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.04%	0.00%	NA
All Japonica	1512	72.00%	24.20%	3.84%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	99.80%	0.00%	0.17%	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	48.10%	44.60%	7.30%	0.00%	NA
Tropical Japonica	504	98.60%	1.20%	0.20%	0.00%	NA
Japonica Intermediate	241	92.10%	7.50%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	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
vg0314845815	A -> G	LOC_Os03g25940.1	downstream_gene_variant ; 4471.0bp to feature; MODIFIER	silent_mutation	Average:52.712; most accessible tissue: Callus, score: 73.753	N	N	N	N
vg0314845815	A -> G	LOC_Os03g25940.4	downstream_gene_variant ; 4471.0bp to feature; MODIFIER	silent_mutation	Average:52.712; most accessible tissue: Callus, score: 73.753	N	N	N	N
vg0314845815	A -> G	LOC_Os03g25930.1	intron_variant ; MODIFIER	silent_mutation	Average:52.712; most accessible tissue: Callus, score: 73.753	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314845815	NA	3.93E-06	mr1912	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