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Detailed information for vg0333506199:

Variant ID: vg0333506199 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 33506199
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.75, A: 0.25, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

CCTTTTGCTTGAAACTTGTGCAACTTAGCAAATATAGAGAGCTGGTGGTTCAATGTAGGAGGGTAAGAGCTGCACCTGCACCACCTTATTTAGGTTGTGT[T/A]
TAGTTCAAGTTAAAATTAAAAGTTTGGTTGCAATTGGAAAGATGCGACGGAAAAGTTAAAAGTTTATGTGTGTAGAAAAGTTTTGATGTGATGGAAAAGT

Reverse complement sequence

ACTTTTCCATCACATCAAAACTTTTCTACACACATAAACTTTTAACTTTTCCGTCGCATCTTTCCAATTGCAACCAAACTTTTAATTTTAACTTGAACTA[A/T]
ACACAACCTAAATAAGGTGGTGCAGGTGCAGCTCTTACCCTCCTACATTGAACCACCAGCTCTCTATATTTGCTAAGTTGCACAAGTTTCAAGCAAAAGG

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	39.00%	6.70%	1.63%	52.69%	NA
All Indica	2759	7.10%	11.00%	2.65%	79.23%	NA
All Japonica	1512	98.90%	0.30%	0.00%	0.73%	NA
Aus	269	1.50%	1.90%	1.12%	95.54%	NA
Indica I	595	8.60%	19.80%	2.02%	69.58%	NA
Indica II	465	5.20%	3.00%	2.15%	89.68%	NA
Indica III	913	6.90%	10.00%	3.40%	79.74%	NA
Indica Intermediate	786	7.40%	10.30%	2.54%	79.77%	NA
Temperate Japonica	767	99.00%	0.10%	0.00%	0.91%	NA
Tropical Japonica	504	98.60%	0.60%	0.00%	0.79%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	1.00%	0.00%	1.04%	NA
Intermediate	90	57.80%	2.20%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0333506199	T -> A	LOC_Os03g58830.1	upstream_gene_variant ; 1151.0bp to feature; MODIFIER	silent_mutation	Average:58.282; most accessible tissue: Callus, score: 92.731	N	N	N	N
vg0333506199	T -> A	LOC_Os03g58840.1	upstream_gene_variant ; 882.0bp to feature; MODIFIER	silent_mutation	Average:58.282; most accessible tissue: Callus, score: 92.731	N	N	N	N
vg0333506199	T -> A	LOC_Os03g58830-LOC_Os03g58840	intergenic_region ; MODIFIER	silent_mutation	Average:58.282; most accessible tissue: Callus, score: 92.731	N	N	N	N
vg0333506199	T -> DEL	N	N	silent_mutation	Average:58.282; most accessible tissue: Callus, score: 92.731	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0333506199	1.67E-06	NA	mr1723	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
vg0333506199	6.10E-07	2.00E-10	mr1723	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
vg0333506199	3.14E-09	NA	mr1723_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
vg0333506199	7.34E-10	2.92E-16	mr1723_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