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Detailed information for vg0802212244:

Variant ID: vg0802212244 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 2212244
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.94, G: 0.06, others allele: 0.00, population size: 88. )

Flanking Sequence (100 bp) in Reference Genome:

CTATGCATGTTTTGAATTTTAGGGTTGGTTCAGGTATTATAGCTAGCACGAAAAGATAATAAGGTATTCTCTTGTGGTGTAGATGAAGATGAAGATTAAG[T/G]
GTTTTACGTAAAATAAGATGGTATTAATGTATAATTAATTGAGTTTTAATTATTATAAATTTTAAAAATAGATTTATCTGATATTTTAGAACAACTTCCA

Reverse complement sequence

TGGAAGTTGTTCTAAAATATCAGATAAATCTATTTTTAAAATTTATAATAATTAAAACTCAATTAATTATACATTAATACCATCTTATTTTACGTAAAAC[A/C]
CTTAATCTTCATCTTCATCTACACCACAAGAGAATACCTTATTATCTTTTCGTGCTAGCTATAATACCTGAACCAACCCTAAAATTCAAAACATGCATAG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.10%	36.00%	0.83%	0.99%	NA
All Indica	2759	39.70%	59.60%	0.58%	0.14%	NA
All Japonica	1512	98.30%	1.70%	0.00%	0.07%	NA
Aus	269	74.30%	1.50%	8.55%	15.61%	NA
Indica I	595	39.30%	60.00%	0.67%	0.00%	NA
Indica II	465	16.60%	83.20%	0.22%	0.00%	NA
Indica III	913	43.70%	56.10%	0.22%	0.00%	NA
Indica Intermediate	786	49.10%	49.20%	1.15%	0.51%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.20%	0.00%	0.20%	NA
Japonica Intermediate	241	97.50%	2.50%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	66.70%	33.30%	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
vg0802212244	T -> G	LOC_Os08g04490.1	downstream_gene_variant ; 2555.0bp to feature; MODIFIER	silent_mutation	Average:41.44; most accessible tissue: Callus, score: 64.231	N	N	N	N
vg0802212244	T -> G	LOC_Os08g04500.1	intron_variant ; MODIFIER	silent_mutation	Average:41.44; most accessible tissue: Callus, score: 64.231	N	N	N	N
vg0802212244	T -> G	LOC_Os08g04500.2	intron_variant ; MODIFIER	silent_mutation	Average:41.44; most accessible tissue: Callus, score: 64.231	N	N	N	N
vg0802212244	T -> DEL	N	N	silent_mutation	Average:41.44; most accessible tissue: Callus, score: 64.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0802212244	NA	9.64E-06	mr1011	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
vg0802212244	NA	4.70E-14	mr1183	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
vg0802212244	NA	6.06E-09	mr1352	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
vg0802212244	NA	7.80E-14	mr1503	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
vg0802212244	NA	3.02E-07	mr1593	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
vg0802212244	NA	7.81E-11	mr1720	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
vg0802212244	6.09E-37	7.88E-30	mr1739	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
vg0802212244	7.67E-36	8.44E-65	mr1739	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
vg0802212244	NA	1.66E-20	mr1183_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
vg0802212244	NA	6.39E-07	mr1268_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
vg0802212244	NA	7.22E-09	mr1319_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
vg0802212244	NA	3.73E-19	mr1352_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
vg0802212244	NA	2.55E-14	mr1720_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
vg0802212244	3.58E-38	1.41E-30	mr1739_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
vg0802212244	3.14E-43	6.11E-75	mr1739_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
vg0802212244	NA	3.20E-09	mr1751_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