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Detailed information for vg0122048209:

Variant ID: vg0122048209 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 22048209
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGCTTCCGCAATAGAAGAGATTGTCATGACCGTCACAATTGCTGCATGTTTGCCCCATTTGTATGTGGTTAGCCTTCTATTTTCTTCTCATTAGAGAC[G/T]
GCTACAACATCTTTGATTTAACAAGATAGATCTATGTTTCTTTTTTGAAAAAAAAGTAATCATTGTCGGATCAATGTTTTGGAGAAAGAAAAAAGGGGAA

Reverse complement sequence

TTCCCCTTTTTTCTTTCTCCAAAACATTGATCCGACAATGATTACTTTTTTTTCAAAAAAGAAACATAGATCTATCTTGTTAAATCAAAGATGTTGTAGC[C/A]
GTCTCTAATGAGAAGAAAATAGAAGGCTAACCACATACAAATGGGGCAAACATGCAGCAATTGTGACGGTCATGACAATCTCTTCTATTGCGGAAGCTCA

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	90.50%	5.70%	3.85%	0.00%	NA
All Indica	2759	99.50%	0.30%	0.22%	0.00%	NA
All Japonica	1512	72.00%	16.90%	11.11%	0.00%	NA
Aus	269	98.50%	0.00%	1.49%	0.00%	NA
Indica I	595	99.70%	0.20%	0.17%	0.00%	NA
Indica II	465	98.70%	1.10%	0.22%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	99.40%	0.30%	0.38%	0.00%	NA
Temperate Japonica	767	51.50%	30.00%	18.51%	0.00%	NA
Tropical Japonica	504	97.20%	1.20%	1.59%	0.00%	NA
Japonica Intermediate	241	84.20%	8.30%	7.47%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	5.60%	4.44%	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
vg0122048209	G -> T	LOC_Os01g39180.1	downstream_gene_variant ; 2895.0bp to feature; MODIFIER	silent_mutation	Average:36.685; most accessible tissue: Callus, score: 59.803	N	N	N	N
vg0122048209	G -> T	LOC_Os01g39190.1	intron_variant ; MODIFIER	silent_mutation	Average:36.685; most accessible tissue: Callus, score: 59.803	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0122048209	NA	8.21E-06	mr1026	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
vg0122048209	NA	3.03E-06	mr1069	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
vg0122048209	NA	2.73E-07	mr1077	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
vg0122048209	NA	2.28E-07	mr1163	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
vg0122048209	NA	4.96E-07	mr1164	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
vg0122048209	NA	2.58E-06	mr1202	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
vg0122048209	NA	1.17E-07	mr1330	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
vg0122048209	NA	2.69E-06	mr1503	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
vg0122048209	NA	1.12E-08	mr1548	Jap_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
vg0122048209	9.56E-07	1.99E-11	mr1627	Jap_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