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Detailed information for vg0222612950:

Variant ID: vg0222612950 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22612950
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.99, T: 0.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TTCAGTAGGCTTATGGCCTGTTTGTATTGTTTGCTTTGTATGTCGCTTAGATTCCGGCTCTCCCGATGTTCCGGTGTACTTTGAAATAGTCGTCGAGGTT[C/T]
CTCCAGGAGCATAGCAAGGCAAGTCATGCTTGTCACTTGAACATATTGATCCTATATTGCAAATGCTCTATCATTTTCCTTTAAGTACTGCATCATTTTA

Reverse complement sequence

TAAAATGATGCAGTACTTAAAGGAAAATGATAGAGCATTTGCAATATAGGATCAATATGTTCAAGTGACAAGCATGACTTGCCTTGCTATGCTCCTGGAG[G/A]
AACCTCGACGACTATTTCAAAGTACACCGGAACATCGGGAGAGCCGGAATCTAAGCGACATACAAAGCAAACAATACAAACAGGCCATAAGCCTACTGAA

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	51.90%	47.90%	0.25%	0.00%	NA
All Indica	2759	82.30%	17.40%	0.36%	0.00%	NA
All Japonica	1512	3.50%	96.40%	0.13%	0.00%	NA
Aus	269	36.40%	63.60%	0.00%	0.00%	NA
Indica I	595	80.30%	19.00%	0.67%	0.00%	NA
Indica II	465	92.30%	7.50%	0.22%	0.00%	NA
Indica III	913	80.90%	18.90%	0.11%	0.00%	NA
Indica Intermediate	786	79.40%	20.10%	0.51%	0.00%	NA
Temperate Japonica	767	0.70%	99.10%	0.26%	0.00%	NA
Tropical Japonica	504	8.50%	91.50%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	33.30%	66.70%	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
vg0222612950	C -> T	LOC_Os02g37450.1	upstream_gene_variant ; 867.0bp to feature; MODIFIER	silent_mutation	Average:39.19; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0222612950	C -> T	LOC_Os02g37460.1	upstream_gene_variant ; 1341.0bp to feature; MODIFIER	silent_mutation	Average:39.19; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0222612950	C -> T	LOC_Os02g37470.1	upstream_gene_variant ; 4553.0bp to feature; MODIFIER	silent_mutation	Average:39.19; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0222612950	C -> T	LOC_Os02g37440.1	downstream_gene_variant ; 3742.0bp to feature; MODIFIER	silent_mutation	Average:39.19; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N
vg0222612950	C -> T	LOC_Os02g37450-LOC_Os02g37460	intergenic_region ; MODIFIER	silent_mutation	Average:39.19; most accessible tissue: Minghui63 panicle, score: 56.842	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222612950	1.77E-06	2.20E-15	mr1188	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
vg0222612950	NA	4.59E-07	mr1188	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
vg0222612950	4.11E-06	1.65E-15	mr1188_2	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
vg0222612950	NA	3.30E-07	mr1968_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