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Detailed information for vg0220807490:

Variant ID: vg0220807490 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20807490
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GGCAGTGGGTCTTTTGGGTTGGAATGGAGCTATGGAGCAATAAAAACCCAGCTCCACCTCGTAGTCCATATTTAAGGAGTAGCTCTGCTAACTTCACTCC[T/C]
AAAAACATAGGATCTAAACCATTTGGCACAACTCCGGCTTAAAGCTGGAGTTAAGAGCTAGAGTTGTGCCAAACATGCCGAAAATGTGCTCTCTCTCTCT

Reverse complement sequence

AGAGAGAGAGAGCACATTTTCGGCATGTTTGGCACAACTCTAGCTCTTAACTCCAGCTTTAAGCCGGAGTTGTGCCAAATGGTTTAGATCCTATGTTTTT[A/G]
GGAGTGAAGTTAGCAGAGCTACTCCTTAAATATGGACTACGAGGTGGAGCTGGGTTTTTATTGCTCCATAGCTCCATTCCAACCCAAAAGACCCACTGCC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.20%	28.80%	0.02%	0.00%	NA
All Indica	2759	98.60%	1.40%	0.00%	0.00%	NA
All Japonica	1512	21.40%	78.60%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	98.10%	1.90%	0.00%	0.00%	NA
Indica III	913	98.70%	1.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.10%	1.90%	0.00%	0.00%	NA
Temperate Japonica	767	6.10%	93.90%	0.00%	0.00%	NA
Tropical Japonica	504	32.50%	67.30%	0.20%	0.00%	NA
Japonica Intermediate	241	46.50%	53.50%	0.00%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	51.10%	48.90%	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
vg0220807490	T -> C	LOC_Os02g34690.1	upstream_gene_variant ; 3850.0bp to feature; MODIFIER	silent_mutation	Average:56.475; most accessible tissue: Callus, score: 81.2	N	N	N	N
vg0220807490	T -> C	LOC_Os02g34680.1	downstream_gene_variant ; 3016.0bp to feature; MODIFIER	silent_mutation	Average:56.475; most accessible tissue: Callus, score: 81.2	N	N	N	N
vg0220807490	T -> C	LOC_Os02g34680-LOC_Os02g34690	intergenic_region ; MODIFIER	silent_mutation	Average:56.475; most accessible tissue: Callus, score: 81.2	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220807490	NA	2.77E-43	mr1563	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
vg0220807490	NA	5.11E-14	mr1128_2	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
vg0220807490	NA	1.16E-08	mr1198_2	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
vg0220807490	NA	4.01E-13	mr1217_2	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
vg0220807490	NA	3.54E-06	mr1232_2	Jap_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
vg0220807490	NA	2.84E-08	mr1275_2	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
vg0220807490	NA	5.20E-07	mr1557_2	Jap_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
vg0220807490	NA	3.82E-15	mr1575_2	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
vg0220807490	2.53E-06	6.46E-48	mr1670_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
vg0220807490	NA	2.71E-07	mr1885_2	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
vg0220807490	NA	1.08E-07	mr1909_2	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
vg0220807490	NA	2.54E-06	mr1944_2	Jap_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