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Detailed information for vg0221475189:

Variant ID: vg0221475189 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21475189
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, C: 0.04, others allele: 0.00, population size: 241. )

Flanking Sequence (100 bp) in Reference Genome:

CGAATTGGTGCTCCTCCAAGTTGCATGGCTTCTTAAAACATACACTGCCTGATGTGAAAACACAGGAAACCATGCAAAGTTTGTGTGGTTTTTTTTCCCC[T/C]
GTCTGCCTAGAGCAGAACTCCCATACAATCTGATCAGGCAGGTGGTGGCTCTGCAGGCCCAGCTGGTTTTGTATTCAGAAGAGGCTGGATTGCCTTCACG

Reverse complement sequence

CGTGAAGGCAATCCAGCCTCTTCTGAATACAAAACCAGCTGGGCCTGCAGAGCCACCACCTGCCTGATCAGATTGTATGGGAGTTCTGCTCTAGGCAGAC[A/G]
GGGGAAAAAAAACCACACAAACTTTGCATGGTTTCCTGTGTTTTCACATCAGGCAGTGTATGTTTTAAGAAGCCATGCAACTTGGAGGAGCACCAATTCG

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	61.10%	38.70%	0.02%	0.13%	NA
All Indica	2759	94.90%	4.90%	0.04%	0.14%	NA
All Japonica	1512	3.70%	96.20%	0.00%	0.07%	NA
Aus	269	63.20%	36.80%	0.00%	0.00%	NA
Indica I	595	98.50%	1.30%	0.00%	0.17%	NA
Indica II	465	96.80%	3.00%	0.00%	0.22%	NA
Indica III	913	91.70%	8.10%	0.11%	0.11%	NA
Indica Intermediate	786	94.80%	5.10%	0.00%	0.13%	NA
Temperate Japonica	767	1.60%	98.30%	0.00%	0.13%	NA
Tropical Japonica	504	6.70%	93.30%	0.00%	0.00%	NA
Japonica Intermediate	241	4.10%	95.90%	0.00%	0.00%	NA
VI/Aromatic	96	9.40%	90.60%	0.00%	0.00%	NA
Intermediate	90	40.00%	58.90%	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
vg0221475189	T -> DEL	N	N	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35760.1	3_prime_UTR_variant ; 34.0bp to feature; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35750.2	3_prime_UTR_variant ; 1768.0bp to feature; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35760.2	3_prime_UTR_variant ; 34.0bp to feature; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35740.1	upstream_gene_variant ; 4053.0bp to feature; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35750.1	downstream_gene_variant ; 1367.0bp to feature; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N
vg0221475189	T -> C	LOC_Os02g35750.3	intron_variant ; MODIFIER	silent_mutation	Average:68.724; most accessible tissue: Callus, score: 86.199	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221475189	NA	4.76E-28	mr1793	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
vg0221475189	6.03E-06	6.03E-06	mr1918	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
vg0221475189	NA	5.62E-06	mr1911_2	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