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Detailed information for vg0222307984:

Variant ID: vg0222307984 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 22307984
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, T: 0.26, others allele: 0.00, population size: 92. )

Flanking Sequence (100 bp) in Reference Genome:

TTAATCACCATGACTCGCATAAAAAGTGTACTATTTAGGGTTTAGGATAGCTGAATTAATAAATTATTTGATTTGTGTGATAGCTATTTGAGGGTATGAA[T/C]
GGATGAATTAACTTATATAAAGTTCAAATTTTATTTTTATAAAGGGATTCCATGATATATTTTTTTTCACGAAAAGAACCATTTAGAAACTTAGGAAGCG

Reverse complement sequence

CGCTTCCTAAGTTTCTAAATGGTTCTTTTCGTGAAAAAAAATATATCATGGAATCCCTTTATAAAAATAAAATTTGAACTTTATATAAGTTAATTCATCC[A/G]
TTCATACCCTCAAATAGCTATCACACAAATCAAATAATTTATTAATTCAGCTATCCTAAACCCTAAATAGTACACTTTTTATGCGAGTCATGGTGATTAA

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	33.90%	10.00%	0.51%	55.63%	NA
All Indica	2759	8.00%	3.10%	0.80%	88.04%	NA
All Japonica	1512	83.90%	11.40%	0.00%	4.63%	NA
Aus	269	0.70%	72.50%	0.37%	26.39%	NA
Indica I	595	16.30%	1.50%	1.34%	80.84%	NA
Indica II	465	1.70%	3.20%	1.08%	93.98%	NA
Indica III	913	3.60%	2.70%	0.22%	93.43%	NA
Indica Intermediate	786	10.70%	4.70%	0.89%	83.72%	NA
Temperate Japonica	767	79.30%	19.30%	0.00%	1.43%	NA
Tropical Japonica	504	89.10%	0.40%	0.00%	10.52%	NA
Japonica Intermediate	241	88.00%	9.50%	0.00%	2.49%	NA
VI/Aromatic	96	65.60%	12.50%	0.00%	21.88%	NA
Intermediate	90	48.90%	7.80%	1.11%	42.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0222307984	T -> DEL	N	N	silent_mutation	Average:31.047; most accessible tissue: Callus, score: 56.112	N	N	N	N
vg0222307984	T -> C	LOC_Os02g36940.1	downstream_gene_variant ; 3849.0bp to feature; MODIFIER	silent_mutation	Average:31.047; most accessible tissue: Callus, score: 56.112	N	N	N	N
vg0222307984	T -> C	LOC_Os02g36924-LOC_Os02g36940	intergenic_region ; MODIFIER	silent_mutation	Average:31.047; most accessible tissue: Callus, score: 56.112	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0222307984	NA	1.20E-06	mr1762	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
vg0222307984	NA	3.49E-12	mr1927	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
vg0222307984	4.61E-07	NA	mr1087_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
vg0222307984	NA	9.53E-06	mr1201_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
vg0222307984	NA	7.76E-06	mr1344_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
vg0222307984	NA	2.85E-08	mr1347_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