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Detailed information for vg0100619688:

Variant ID: vg0100619688 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 619688
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, A: 0.01, others allele: 0.00, population size: 124. )

Flanking Sequence (100 bp) in Reference Genome:

TTTTGATTAATCTCGTATTGGGTTCTTATATGGAAACTTCTTTCAATATTGCTTATTTTTAATTCCAAATTTCAGCTATTTTAAAATTGTATTTCTACTT[G/A]
GGTCTCTTTTTTTCTTTCTAATTTTGGATTTTATTTTATTTTTATTTCGAATTTCGATTAATCTTGTATTGGGTTCTTATATGGAAACTTCTTTCAATAT

Reverse complement sequence

ATATTGAAAGAAGTTTCCATATAAGAACCCAATACAAGATTAATCGAAATTCGAAATAAAAATAAAATAAAATCCAAAATTAGAAAGAAAAAAAGAGACC[C/T]
AAGTAGAAATACAATTTTAAAATAGCTGAAATTTGGAATTAAAAATAAGCAATATTGAAAGAAGTTTCCATATAAGAACCCAATACGAGATTAATCAAAA

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	51.00%	33.50%	2.60%	12.89%	NA
All Indica	2759	24.00%	51.80%	2.94%	21.31%	NA
All Japonica	1512	92.80%	5.40%	1.59%	0.26%	NA
Aus	269	75.50%	17.80%	6.69%	0.00%	NA
Indica I	595	10.80%	87.20%	0.67%	1.34%	NA
Indica II	465	22.20%	12.00%	2.80%	63.01%	NA
Indica III	913	29.70%	56.20%	3.83%	10.30%	NA
Indica Intermediate	786	28.40%	43.40%	3.69%	24.55%	NA
Temperate Japonica	767	87.50%	8.90%	3.13%	0.52%	NA
Tropical Japonica	504	99.40%	0.60%	0.00%	0.00%	NA
Japonica Intermediate	241	95.90%	4.10%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	9.40%	0.00%	3.12%	NA
Intermediate	90	65.60%	18.90%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0100619688	G -> A	LOC_Os01g02139.1	upstream_gene_variant ; 4399.0bp to feature; MODIFIER	silent_mutation	Average:15.628; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0100619688	G -> A	LOC_Os01g02120.1	downstream_gene_variant ; 4038.0bp to feature; MODIFIER	silent_mutation	Average:15.628; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0100619688	G -> A	LOC_Os01g02130.1	downstream_gene_variant ; 884.0bp to feature; MODIFIER	silent_mutation	Average:15.628; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0100619688	G -> A	LOC_Os01g02120-LOC_Os01g02130	intergenic_region ; MODIFIER	silent_mutation	Average:15.628; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N
vg0100619688	G -> DEL	N	N	silent_mutation	Average:15.628; most accessible tissue: Zhenshan97 panicle, score: 39.652	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0100619688	NA	3.12E-06	mr1269	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
vg0100619688	NA	2.25E-07	mr1603	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