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Detailed information for vg0315566044:

Variant ID: vg0315566044 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 15566044
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCCGACAATGGCCATGCGCTTGCCCCGCCTGGTCTCGTGTTGCCCATGTTAGGAAACGATAGGCAAATAAACAATAAAGAACAATAGGTCAATCACAG[A/G]
AGACACGAGATTTAACGTGAAAAACCTTCCCAAAGCAGGAGAGAAAAAAGCATGGGCGCCAGCCAACAAAAATATCTTCACTATATCGGGGTAAGGTTAC

Reverse complement sequence

GTAACCTTACCCCGATATAGTGAAGATATTTTTGTTGGCTGGCGCCCATGCTTTTTTCTCTCCTGCTTTGGGAAGGTTTTTCACGTTAAATCTCGTGTCT[T/C]
CTGTGATTGACCTATTGTTCTTTATTGTTTATTTGCCTATCGTTTCCTAACATGGGCAACACGAGACCAGGCGGGGCAAGCGCATGGCCATTGTCGGGCA

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	84.40%	14.60%	0.93%	0.00%	NA
All Indica	2759	78.80%	20.80%	0.43%	0.00%	NA
All Japonica	1512	90.90%	7.00%	2.05%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	40.50%	58.20%	1.34%	0.00%	NA
Indica II	465	97.60%	2.40%	0.00%	0.00%	NA
Indica III	913	87.40%	12.60%	0.00%	0.00%	NA
Indica Intermediate	786	86.60%	12.80%	0.51%	0.00%	NA
Temperate Japonica	767	95.70%	2.20%	2.09%	0.00%	NA
Tropical Japonica	504	90.10%	9.70%	0.20%	0.00%	NA
Japonica Intermediate	241	77.60%	16.60%	5.81%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	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
vg0315566044	A -> G	LOC_Os03g27170.1	upstream_gene_variant ; 1117.0bp to feature; MODIFIER	silent_mutation	Average:63.72; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0315566044	A -> G	LOC_Os03g27160.1	downstream_gene_variant ; 3483.0bp to feature; MODIFIER	silent_mutation	Average:63.72; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0315566044	A -> G	LOC_Os03g27190.1	downstream_gene_variant ; 1855.0bp to feature; MODIFIER	silent_mutation	Average:63.72; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0315566044	A -> G	LOC_Os03g27170-LOC_Os03g27190	intergenic_region ; MODIFIER	silent_mutation	Average:63.72; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0315566044	NA	1.14E-06	mr1180	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
vg0315566044	NA	1.02E-08	mr1274	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
vg0315566044	NA	1.86E-07	mr1274	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
vg0315566044	NA	9.24E-10	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
vg0315566044	NA	7.16E-06	mr1113_2	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
vg0315566044	NA	6.99E-08	mr1695_2	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
vg0315566044	NA	8.73E-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
vg0315566044	NA	5.87E-06	mr1865_2	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