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Detailed information for vg0208440052:

Variant ID: vg0208440052 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8440052
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.94, A: 0.06, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TGCTATTAAAACAAGCAAGAATTGTACGCGACCAATGACAAGAGTTATGTCAACAATCTCACCTAGCTATGTACATAGACAACATATCCTATGCACACAT[G/A]
CCCTCACGTGTACACACGTGCACACCAACTAAAAAATGTCACAAAAAAATCTAGAAAAAATCATACACATACTTTCAATTATATTACACCTAGGGGTTAA

Reverse complement sequence

TTAACCCCTAGGTGTAATATAATTGAAAGTATGTGTATGATTTTTTCTAGATTTTTTTGTGACATTTTTTAGTTGGTGTGCACGTGTGTACACGTGAGGG[C/T]
ATGTGTGCATAGGATATGTTGTCTATGTACATAGCTAGGTGAGATTGTTGACATAACTCTTGTCATTGGTCGCGTACAATTCTTGCTTGTTTTAATAGCA

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	60.80%	23.20%	0.95%	15.02%	NA
All Indica	2759	53.10%	30.00%	1.30%	15.62%	NA
All Japonica	1512	71.30%	12.00%	0.46%	16.20%	NA
Aus	269	73.20%	26.40%	0.00%	0.37%	NA
Indica I	595	38.80%	25.20%	2.35%	33.61%	NA
Indica II	465	68.80%	22.60%	0.65%	7.96%	NA
Indica III	913	53.50%	36.10%	0.77%	9.64%	NA
Indica Intermediate	786	54.20%	30.80%	1.53%	13.49%	NA
Temperate Japonica	767	78.70%	18.60%	0.26%	2.35%	NA
Tropical Japonica	504	55.40%	2.00%	0.79%	41.87%	NA
Japonica Intermediate	241	80.90%	12.00%	0.41%	6.64%	NA
VI/Aromatic	96	72.90%	1.00%	2.08%	23.96%	NA
Intermediate	90	72.20%	16.70%	0.00%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208440052	G -> A	LOC_Os02g15140.1	downstream_gene_variant ; 3345.0bp to feature; MODIFIER	silent_mutation	Average:36.522; most accessible tissue: Callus, score: 54.5	N	N	N	N
vg0208440052	G -> A	LOC_Os02g15140-LOC_Os02g15150	intergenic_region ; MODIFIER	silent_mutation	Average:36.522; most accessible tissue: Callus, score: 54.5	N	N	N	N
vg0208440052	G -> DEL	N	N	silent_mutation	Average:36.522; most accessible tissue: Callus, score: 54.5	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208440052	1.05E-07	1.05E-07	mr1883	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