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Detailed information for vg0401992281:

Variant ID: vg0401992281 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1992281
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.86, T: 0.14, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

GGCCAAAATTGTCAGAGTTGGGATCCTATCCCAGAGATGCACAACAATGCAAACAAAGTAAGCACAACAAAACCTATTGTCTGATTGCCATTTACAAAAT[A/T]
ACAGTTCAAGCCATTTCAAATATCTCTACTATTATAAAAATTGAAGATGTTTCCACCGGAATTTTGGTACGTATCCAATTCGACATGAGTCTAAAATAAC

Reverse complement sequence

GTTATTTTAGACTCATGTCGAATTGGATACGTACCAAAATTCCGGTGGAAACATCTTCAATTTTTATAATAGTAGAGATATTTGAAATGGCTTGAACTGT[T/A]
ATTTTGTAAATGGCAATCAGACAATAGGTTTTGTTGTGCTTACTTTGTTTGCATTGTTGTGCATCTCTGGGATAGGATCCCAACTCTGACAATTTTGGCC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.90%	43.30%	0.78%	0.00%	NA
All Indica	2759	53.70%	45.30%	1.01%	0.00%	NA
All Japonica	1512	59.30%	40.20%	0.46%	0.00%	NA
Aus	269	53.90%	46.10%	0.00%	0.00%	NA
Indica I	595	28.10%	71.80%	0.17%	0.00%	NA
Indica II	465	34.40%	61.90%	3.66%	0.00%	NA
Indica III	913	80.20%	19.30%	0.55%	0.00%	NA
Indica Intermediate	786	53.80%	45.50%	0.64%	0.00%	NA
Temperate Japonica	767	48.50%	50.80%	0.65%	0.00%	NA
Tropical Japonica	504	63.10%	36.70%	0.20%	0.00%	NA
Japonica Intermediate	241	85.90%	13.70%	0.41%	0.00%	NA
VI/Aromatic	96	86.50%	13.50%	0.00%	0.00%	NA
Intermediate	90	40.00%	57.80%	2.22%	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
vg0401992281	A -> T	LOC_Os04g04254.1	intron_variant ; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N
vg0401992281	A -> T	LOC_Os04g04254.2	intron_variant ; MODIFIER	silent_mutation	Average:38.789; most accessible tissue: Minghui63 flag leaf, score: 58.568	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401992281	1.20E-09	NA	mr1798_2	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
vg0401992281	NA	3.47E-09	mr1798_2	Ind_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251