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Detailed information for vg0217864370:

Variant ID: vg0217864370 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 17864370
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, C: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:

TCGCATGTTTGCGAAAAGATATATCACATATTGATCCATCTTGATAATTTTTTAAAATTTTTTATAACTTTTTAAACGCCATGCACAAAACAAGGGGATG[T/C]
TGTCTCAAGGGAAAAAAAATCCACTTCCCTATTAAGCAGGCTCAATTTGAGCTCATGCAGTCGAGCTGGGCAGTAAGTAGTATATAGTATATAAGTGTAT

Reverse complement sequence

ATACACTTATATACTATATACTACTTACTGCCCAGCTCGACTGCATGAGCTCAAATTGAGCCTGCTTAATAGGGAAGTGGATTTTTTTTCCCTTGAGACA[A/G]
CATCCCCTTGTTTTGTGCATGGCGTTTAAAAAGTTATAAAAAATTTTAAAAAATTATCAAGATGGATCAATATGTGATATATCTTTTCGCAAACATGCGA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.40%	7.10%	2.14%	0.38%	NA
All Indica	2759	90.70%	9.20%	0.07%	0.00%	NA
All Japonica	1512	92.30%	0.20%	6.42%	1.12%	NA
Aus	269	75.10%	24.90%	0.00%	0.00%	NA
Indica I	595	91.10%	8.60%	0.34%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	87.60%	12.40%	0.00%	0.00%	NA
Indica Intermediate	786	90.30%	9.70%	0.00%	0.00%	NA
Temperate Japonica	767	85.80%	0.00%	12.13%	2.09%	NA
Tropical Japonica	504	99.20%	0.40%	0.40%	0.00%	NA
Japonica Intermediate	241	98.30%	0.40%	0.83%	0.41%	NA
VI/Aromatic	96	92.70%	5.20%	2.08%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0217864370	T -> DEL	N	N	silent_mutation	Average:33.876; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0217864370	T -> C	LOC_Os02g30090.1	upstream_gene_variant ; 3534.0bp to feature; MODIFIER	silent_mutation	Average:33.876; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0217864370	T -> C	LOC_Os02g30070.1	downstream_gene_variant ; 4250.0bp to feature; MODIFIER	silent_mutation	Average:33.876; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N
vg0217864370	T -> C	LOC_Os02g30080.1	intron_variant ; MODIFIER	silent_mutation	Average:33.876; most accessible tissue: Zhenshan97 panicle, score: 59.59	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0217864370	4.42E-07	1.04E-06	mr1057	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
vg0217864370	7.72E-07	NA	mr1272	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
vg0217864370	9.86E-06	NA	mr1275	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
vg0217864370	5.55E-06	NA	mr1306	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
vg0217864370	3.50E-06	3.50E-06	mr1357	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
vg0217864370	3.17E-06	1.19E-06	mr1590	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
vg0217864370	NA	3.96E-06	mr1738	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
vg0217864370	3.58E-06	1.65E-06	mr1755	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