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Detailed information for vg0134125967:

Variant ID: vg0134125967 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 34125967
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, G: 0.23, others allele: 0.00, population size: 163. )

Flanking Sequence (100 bp) in Reference Genome:

TACAGAGTTTACTACAAAGCCATGACAACTTAAGCACCTTGTGCCAAACATTATACACCAAAAGGCCTAACCACTCTCCTTCAAACCAATCCTAATAACA[T/G]
ATGTACTACCCCCAAAACCCTGAAATGGGATGAGATCACCCTGCCTGAGAAATGGGTTTTATCTCAAGCTGTTGAACCTAAGTCTATGGATCAATCAGAA

Reverse complement sequence

TTCTGATTGATCCATAGACTTAGGTTCAACAGCTTGAGATAAAACCCATTTCTCAGGCAGGGTGATCTCATCCCATTTCAGGGTTTTGGGGGTAGTACAT[A/C]
TGTTATTAGGATTGGTTTGAAGGAGAGTGGTTAGGCCTTTTGGTGTATAATGTTTGGCACAAGGTGCTTAAGTTGTCATGGCTTTGTAGTAAACTCTGTA

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	51.70%	7.00%	27.99%	13.37%	NA
All Indica	2759	33.40%	10.70%	34.51%	21.38%	NA
All Japonica	1512	89.00%	1.00%	9.99%	0.00%	NA
Aus	269	4.80%	6.30%	76.58%	12.27%	NA
Indica I	595	24.70%	6.90%	23.19%	45.21%	NA
Indica II	465	75.70%	2.20%	18.06%	4.09%	NA
Indica III	913	10.30%	21.70%	52.25%	15.77%	NA
Indica Intermediate	786	41.90%	5.90%	32.19%	20.10%	NA
Temperate Japonica	767	90.50%	0.30%	9.26%	0.00%	NA
Tropical Japonica	504	92.70%	1.00%	6.35%	0.00%	NA
Japonica Intermediate	241	76.80%	3.30%	19.92%	0.00%	NA
VI/Aromatic	96	94.80%	0.00%	3.12%	2.08%	NA
Intermediate	90	76.70%	3.30%	12.22%	7.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0134125967	T -> G	LOC_Os01g59040.1	upstream_gene_variant ; 642.0bp to feature; MODIFIER	silent_mutation	Average:21.364; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg0134125967	T -> G	LOC_Os01g59040-LOC_Os01g59050	intergenic_region ; MODIFIER	silent_mutation	Average:21.364; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N
vg0134125967	T -> DEL	N	N	silent_mutation	Average:21.364; most accessible tissue: Zhenshan97 root, score: 38.035	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0134125967	NA	5.14E-07	mr1044	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
vg0134125967	NA	3.84E-06	mr1352	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
vg0134125967	4.36E-06	4.34E-06	mr1856	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
vg0134125967	NA	1.11E-06	mr1015_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
vg0134125967	NA	8.78E-07	mr1060_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
vg0134125967	NA	6.08E-06	mr1060_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
vg0134125967	NA	7.82E-06	mr1064_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
vg0134125967	NA	1.69E-08	mr1268_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
vg0134125967	NA	4.74E-09	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
vg0134125967	NA	7.12E-06	mr1319_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
vg0134125967	NA	3.76E-06	mr1332_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
vg0134125967	NA	4.46E-10	mr1478_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
vg0134125967	NA	2.73E-08	mr1478_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
vg0134125967	NA	7.75E-07	mr1971_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