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Detailed information for vg0210463160:

Variant ID: vg0210463160 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 10463160
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.86, T: 0.15, others allele: 0.00, population size: 59. )

Flanking Sequence (100 bp) in Reference Genome:

TTCGTTTTTTCCCTTTTTTTGTCGTTTCTATTCGGTTGTTTTTTTCTTTTTTTCTCTTTTTTTTCTCCGTTTTTCTCGTTTCTTTTCGGTTTGGTTTTTT[C/T]
ATTTTTTTTTCCGGTTTCTCTTGTATTTCTTTTTCTGGTTTTTTAAAGATGCATGAATATAAAGTATGTATTCGTATGTATGCAAAGTTTGTATTCGTAC

Reverse complement sequence

GTACGAATACAAACTTTGCATACATACGAATACATACTTTATATTCATGCATCTTTAAAAAACCAGAAAAAGAAATACAAGAGAAACCGGAAAAAAAAAT[G/A]
AAAAAACCAAACCGAAAAGAAACGAGAAAAACGGAGAAAAAAAAGAGAAAAAAAGAAAAAAACAACCGAATAGAAACGACAAAAAAAGGGAAAAAACGAA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.60%	4.00%	0.42%	41.01%	NA
All Indica	2759	28.60%	6.60%	0.65%	64.19%	NA
All Japonica	1512	98.70%	0.10%	0.00%	1.26%	NA
Aus	269	55.40%	0.70%	0.00%	43.87%	NA
Indica I	595	35.50%	13.30%	0.50%	50.76%	NA
Indica II	465	16.60%	7.70%	0.86%	74.84%	NA
Indica III	913	34.50%	0.20%	0.33%	64.95%	NA
Indica Intermediate	786	23.70%	8.10%	1.02%	67.18%	NA
Temperate Japonica	767	99.00%	0.00%	0.00%	1.04%	NA
Tropical Japonica	504	98.00%	0.20%	0.00%	1.79%	NA
Japonica Intermediate	241	99.20%	0.00%	0.00%	0.83%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	62.20%	3.30%	2.22%	32.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0210463160	C -> T	LOC_Os02g18030.1	upstream_gene_variant ; 3264.0bp to feature; MODIFIER	silent_mutation	Average:29.769; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0210463160	C -> T	LOC_Os02g18040.1	upstream_gene_variant ; 1369.0bp to feature; MODIFIER	silent_mutation	Average:29.769; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0210463160	C -> T	LOC_Os02g18020.1	downstream_gene_variant ; 4571.0bp to feature; MODIFIER	silent_mutation	Average:29.769; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0210463160	C -> T	LOC_Os02g18030-LOC_Os02g18040	intergenic_region ; MODIFIER	silent_mutation	Average:29.769; most accessible tissue: Zhenshan97 panicle, score: 75.67	N	N	N	N
vg0210463160	C -> DEL	N	N	silent_mutation	Average:29.769; 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
vg0210463160	2.37E-09	4.17E-14	mr1172_2	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
vg0210463160	8.83E-08	5.11E-09	mr1172_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