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Detailed information for vg0142695483:

Variant ID: vg0142695483 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 42695483
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TGAGAAGATGGCCTTACACATATCATACTCAGTTACTCAGGCCTGAATGGCAAGTTGAGATTGTAATGCTTATATTGAAATTCCATCCAACCACAGCCGG[A/G]
TCAACAAATGAAATAAATGGCCATCCAAAATTGTTTCGCCAAGATCACATCGGTAAATTCCAACATTCTACAGGTGTTCCAGAATCTCGCCACAAAATAA

Reverse complement sequence

TTATTTTGTGGCGAGATTCTGGAACACCTGTAGAATGTTGGAATTTACCGATGTGATCTTGGCGAAACAATTTTGGATGGCCATTTATTTCATTTGTTGA[T/C]
CCGGCTGTGGTTGGATGGAATTTCAATATAAGCATTACAATCTCAACTTGCCATTCAGGCCTGAGTAACTGAGTATGATATGTGTAAGGCCATCTTCTCA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	87.50%	12.50%	0.06%	0.00%	NA
All Indica	2759	79.10%	20.80%	0.07%	0.00%	NA
All Japonica	1512	99.70%	0.30%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	91.60%	8.40%	0.00%	0.00%	NA
Indica II	465	36.30%	63.70%	0.00%	0.00%	NA
Indica III	913	90.50%	9.50%	0.00%	0.00%	NA
Indica Intermediate	786	81.70%	18.10%	0.25%	0.00%	NA
Temperate Japonica	767	99.70%	0.30%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	10.00%	1.11%	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
vg0142695483	A -> G	LOC_Os01g73680.1	3_prime_UTR_variant ; 286.0bp to feature; MODIFIER	silent_mutation	Average:64.648; most accessible tissue: Callus, score: 88.135	N	N	N	N
vg0142695483	A -> G	LOC_Os01g73690.1	3_prime_UTR_variant ; 443.0bp to feature; MODIFIER	silent_mutation	Average:64.648; most accessible tissue: Callus, score: 88.135	N	N	N	N
vg0142695483	A -> G	LOC_Os01g73700.1	downstream_gene_variant ; 4488.0bp to feature; MODIFIER	silent_mutation	Average:64.648; most accessible tissue: Callus, score: 88.135	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0142695483	NA	1.05E-06	mr1749	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
vg0142695483	NA	4.60E-06	mr1919	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
vg0142695483	NA	7.85E-07	mr1919	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
vg0142695483	1.13E-13	2.22E-20	mr1974	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
vg0142695483	2.31E-12	9.49E-20	mr1974	Ind_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
vg0142695483	1.89E-06	7.52E-07	mr1984	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
vg0142695483	1.30E-06	5.34E-09	mr1984	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
vg0142695483	NA	4.17E-07	mr1188_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
vg0142695483	NA	2.41E-10	mr1322_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
vg0142695483	NA	4.00E-06	mr1322_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
vg0142695483	NA	1.97E-08	mr1449_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
vg0142695483	NA	1.89E-06	mr1497_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
vg0142695483	NA	5.50E-07	mr1498_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
vg0142695483	NA	7.67E-10	mr1527_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
vg0142695483	NA	3.58E-06	mr1527_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
vg0142695483	NA	8.71E-06	mr1928_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
vg0142695483	NA	3.00E-06	mr1931_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
vg0142695483	NA	2.44E-06	mr1942_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
vg0142695483	1.48E-11	9.15E-17	mr1974_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
vg0142695483	1.17E-10	3.59E-15	mr1974_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