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Detailed information for vg0116932562:

Variant ID: vg0116932562 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 16932562
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, T: 0.00, others allele: 0.00, population size: 204. )

Flanking Sequence (100 bp) in Reference Genome:

AGTGCAACCAAACTAAATCACCCGGTTCAAGCTTAACCTCTTGCCTACCTTTACTACCAACAATTCTATACTTTTCAGTCATCTTTTCAATGTTGAGCTT[G/T]
GTTGACTCATGCATTTTCAAAATAAATTCAGCGCGTGCCTTAGCATCATGATGAACCCTCTCACTAGTAGGTAAAGGCAAAATATCAATTGGAGCACGAG

Reverse complement sequence

CTCGTGCTCCAATTGATATTTTGCCTTTACCTACTAGTGAGAGGGTTCATCATGATGCTAAGGCACGCGCTGAATTTATTTTGAAAATGCATGAGTCAAC[C/A]
AAGCTCAACATTGAAAAGATGACTGAAAAGTATAGAATTGTTGGTAGTAAAGGTAGGCAAGAGGTTAAGCTTGAACCGGGTGATTTAGTTTGGTTGCACT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	52.90%	2.20%	16.36%	28.59%	NA
All Indica	2759	25.00%	3.30%	24.72%	46.97%	NA
All Japonica	1512	99.10%	0.00%	0.26%	0.60%	NA
Aus	269	53.20%	4.50%	29.37%	13.01%	NA
Indica I	595	29.90%	5.90%	19.16%	45.04%	NA
Indica II	465	28.80%	1.30%	15.27%	54.62%	NA
Indica III	913	14.00%	3.10%	33.73%	49.18%	NA
Indica Intermediate	786	31.70%	2.90%	24.05%	41.35%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	97.60%	0.00%	0.60%	1.79%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	80.00%	0.00%	8.89%	11.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0116932562	G -> T	LOC_Os01g30970.1	downstream_gene_variant ; 2842.0bp to feature; MODIFIER	silent_mutation	Average:6.553; most accessible tissue: Callus, score: 19.307	N	N	N	N
vg0116932562	G -> T	LOC_Os01g30980.1	intron_variant ; MODIFIER	silent_mutation	Average:6.553; most accessible tissue: Callus, score: 19.307	N	N	N	N
vg0116932562	G -> DEL	N	N	silent_mutation	Average:6.553; most accessible tissue: Callus, score: 19.307	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0116932562	NA	3.87E-06	mr1215	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
vg0116932562	NA	6.34E-06	mr1378	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
vg0116932562	NA	4.33E-07	mr1511	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
vg0116932562	NA	7.82E-06	mr1534	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
vg0116932562	NA	3.97E-10	mr1707	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
vg0116932562	1.58E-06	1.22E-11	mr1728	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
vg0116932562	NA	1.41E-07	mr1728	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
vg0116932562	NA	4.09E-11	mr1860	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
vg0116932562	NA	2.77E-06	mr1860	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
vg0116932562	NA	5.22E-07	mr1881	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
vg0116932562	NA	2.14E-09	mr1707_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
vg0116932562	NA	4.27E-06	mr1707_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
vg0116932562	NA	1.29E-11	mr1728_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
vg0116932562	NA	4.98E-06	mr1728_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
vg0116932562	NA	1.04E-09	mr1860_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
vg0116932562	NA	3.56E-06	mr1860_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