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Detailed information for vg0137487606:

Variant ID: vg0137487606 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 37487606
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.89, G: 0.10, T: 0.01, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

CCAATTAACGAATTTGTTGTATATTTGTCGACAAATTTTCCTCCAAAAATTTATCAAATGTAATTACAGTATAATCGTAGTGTAATTATGTAACTTTCAA[A/G]
AATCTCTCGGTAACATGTTATTTCAGTAAAATAGAGGTCGTGGGAACAAATCCTTTCACATATGTGTGTGCTGTGATTATTTTTCTTCCTCACTAGAACA

Reverse complement sequence

TGTTCTAGTGAGGAAGAAAAATAATCACAGCACACACATATGTGAAAGGATTTGTTCCCACGACCTCTATTTTACTGAAATAACATGTTACCGAGAGATT[T/C]
TTGAAAGTTACATAATTACACTACGATTATACTGTAATTACATTTGATAAATTTTTGGAGGAAAATTTGTCGACAAATATACAACAAATTCGTTAATTGG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.40%	41.30%	0.25%	0.00%	NA
All Indica	2759	95.50%	4.20%	0.33%	0.00%	NA
All Japonica	1512	1.90%	98.00%	0.13%	0.00%	NA
Aus	269	25.30%	74.70%	0.00%	0.00%	NA
Indica I	595	97.60%	2.00%	0.34%	0.00%	NA
Indica II	465	97.80%	1.90%	0.22%	0.00%	NA
Indica III	913	97.20%	2.60%	0.22%	0.00%	NA
Indica Intermediate	786	90.50%	9.00%	0.51%	0.00%	NA
Temperate Japonica	767	1.40%	98.30%	0.26%	0.00%	NA
Tropical Japonica	504	2.40%	97.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	32.20%	66.70%	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
vg0137487606	A -> G	LOC_Os01g64600.1	upstream_gene_variant ; 3125.0bp to feature; MODIFIER	silent_mutation	Average:80.955; most accessible tissue: Zhenshan97 flower, score: 91.158	N	N	N	N
vg0137487606	A -> G	LOC_Os01g64590-LOC_Os01g64600	intergenic_region ; MODIFIER	silent_mutation	Average:80.955; most accessible tissue: Zhenshan97 flower, score: 91.158	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0137487606	NA	4.91E-24	mr1264	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
vg0137487606	2.27E-07	NA	mr1517	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
vg0137487606	1.74E-06	9.58E-71	mr1538	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
vg0137487606	NA	3.61E-22	mr1541	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
vg0137487606	8.16E-07	NA	mr1672	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
vg0137487606	3.01E-06	3.45E-06	mr1672	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
vg0137487606	NA	5.22E-06	mr1170_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
vg0137487606	NA	1.65E-08	mr1172_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
vg0137487606	NA	8.24E-06	mr1329_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
vg0137487606	NA	8.15E-06	mr1524_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