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Detailed information for vg0117360571:

Variant ID: vg0117360571 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17360571
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.54, A: 0.48, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

GAAAGGATGTATAAGATCTTCTCAAACGCCATCGTTGTCAGCTACTCACACTTGCTGCCAGTCGTACCATTCAATGCATTCAATCCTCCTCCACCGGTAC[A/G]
TATTCATACACTTCAACCTTTCTCAAAATATGATCTTGTTTTCTTGTTGAATCAGTTAACAATGAAGGATATTACACCCAGGAATTTGCTTTGATGAAGT

Reverse complement sequence

ACTTCATCAAAGCAAATTCCTGGGTGTAATATCCTTCATTGTTAACTGATTCAACAAGAAAACAAGATCATATTTTGAGAAAGGTTGAAGTGTATGAATA[T/C]
GTACCGGTGGAGGAGGATTGAATGCATTGAATGGTACGACTGGCAGCAAGTGTGAGTAGCTGACAACGATGGCGTTTGAGAAGATCTTATACATCCTTTC

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	48.90%	40.80%	10.28%	0.00%	NA
All Indica	2759	75.20%	9.00%	15.80%	0.00%	NA
All Japonica	1512	2.50%	96.00%	1.52%	0.00%	NA
Aus	269	58.70%	32.70%	8.55%	0.00%	NA
Indica I	595	83.40%	2.50%	14.12%	0.00%	NA
Indica II	465	87.10%	6.50%	6.45%	0.00%	NA
Indica III	913	67.80%	13.90%	18.29%	0.00%	NA
Indica Intermediate	786	70.70%	9.50%	19.72%	0.00%	NA
Temperate Japonica	767	0.80%	98.80%	0.39%	0.00%	NA
Tropical Japonica	504	1.60%	94.60%	3.77%	0.00%	NA
Japonica Intermediate	241	10.00%	89.60%	0.41%	0.00%	NA
VI/Aromatic	96	6.20%	93.80%	0.00%	0.00%	NA
Intermediate	90	37.80%	57.80%	4.44%	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
vg0117360571	A -> G	LOC_Os01g31714.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:18.916; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N
vg0117360571	A -> G	LOC_Os01g31730.1	downstream_gene_variant ; 2872.0bp to feature; MODIFIER	silent_mutation	Average:18.916; most accessible tissue: Zhenshan97 panicle, score: 28.447	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117360571	NA	2.64E-15	mr1228	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
vg0117360571	NA	1.28E-07	mr1680	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
vg0117360571	NA	2.02E-45	mr1519_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
vg0117360571	NA	1.28E-06	mr1568_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
vg0117360571	4.69E-06	6.16E-06	mr1681_2	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