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Detailed information for vg0825503497:

Variant ID: vg0825503497 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 25503497
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

TTATACCCGAGGTAGGCAGCCTAAAGCCACGAACCAAACTCATACTAGGAGTCTTAAACACCTTAGGAAACCCTCTAGTACAAGAAACAAACTTTACATA[A/T]
CCAATCATACCAAATTTGGACTCCTTCCAAATTCGACTCCGCATCCCATACACACACAATAACTCCATCGTATGCCATATGGAATCTCCATCAACCACGT

Reverse complement sequence

ACGTGGTTGATGGAGATTCCATATGGCATACGATGGAGTTATTGTGTGTGTATGGGATGCGGAGTCGAATTTGGAAGGAGTCCAAATTTGGTATGATTGG[T/A]
TATGTAAAGTTTGTTTCTTGTACTAGAGGGTTTCCTAAGGTGTTTAAGACTCCTAGTATGAGTTTGGTTCGTGGCTTTAGGCTGCCTACCTCGGGTATAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	64.30%	35.60%	0.17%	0.00%	NA
All Indica	2759	50.40%	49.40%	0.22%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	1.50%	98.10%	0.37%	0.00%	NA
Indica I	595	78.30%	21.50%	0.17%	0.00%	NA
Indica II	465	71.80%	28.00%	0.22%	0.00%	NA
Indica III	913	16.90%	82.90%	0.22%	0.00%	NA
Indica Intermediate	786	55.60%	44.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	97.90%	2.10%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	15.60%	1.04%	0.00%	NA
Intermediate	90	67.80%	32.20%	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
vg0825503497	A -> T	LOC_Os08g40280.1	downstream_gene_variant ; 1336.0bp to feature; MODIFIER	silent_mutation	Average:35.53; most accessible tissue: Zhenshan97 flower, score: 52.901	N	N	N	N
vg0825503497	A -> T	LOC_Os08g40290.1	downstream_gene_variant ; 1816.0bp to feature; MODIFIER	silent_mutation	Average:35.53; most accessible tissue: Zhenshan97 flower, score: 52.901	N	N	N	N
vg0825503497	A -> T	LOC_Os08g40280-LOC_Os08g40290	intergenic_region ; MODIFIER	silent_mutation	Average:35.53; most accessible tissue: Zhenshan97 flower, score: 52.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0825503497	NA	1.06E-07	mr1659	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