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Detailed information for vg0117245466:

Variant ID: vg0117245466 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 17245466
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCCTCTGATACAATCTGCATGGAGATGGAGGAGAAATCGACAATCATATGTGACCATGCCACTGCCCCAGAGATTTCAAAATATACATCATGCTGGCG[G/A]
TAAGTACACTCAGGTATGCGAAAGATAAAACAAGGTTCACCATTCCTTTTACTCATAATTATCTTCATTTGAATGAGACTTGATCGTACATGATTATGTT

Reverse complement sequence

AACATAATCATGTACGATCAAGTCTCATTCAAATGAAGATAATTATGAGTAAAAGGAATGGTGAACCTTGTTTTATCTTTCGCATACCTGAGTGTACTTA[C/T]
CGCCAGCATGATGTATATTTTGAAATCTCTGGGGCAGTGGCATGGTCACATATGATTGTCGATTTCTCCTCCATCTCCATGCAGATTGTATCAGAGGAAG

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	97.30%	1.60%	1.10%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.04%	0.00%	NA
All Japonica	1512	92.30%	4.40%	3.37%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	85.50%	8.30%	6.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.00%	0.20%	0.00%	NA
Japonica Intermediate	241	97.90%	0.80%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	6.70%	0.00%	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
vg0117245466	G -> A	LOC_Os01g31520.1	downstream_gene_variant ; 4975.0bp to feature; MODIFIER	silent_mutation	Average:49.316; most accessible tissue: Zhenshan97 flag leaf, score: 75.143	N	N	N	N
vg0117245466	G -> A	LOC_Os01g31520-LOC_Os01g31540	intergenic_region ; MODIFIER	silent_mutation	Average:49.316; most accessible tissue: Zhenshan97 flag leaf, score: 75.143	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0117245466	6.84E-06	6.85E-06	mr1112	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
vg0117245466	1.89E-06	NA	mr1246	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