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Detailed information for vg0220021692:

Variant ID: vg0220021692 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20021692
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.98, T: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CTCGACCACAGTCTCTACTACCCGAAATGTCCTGGAAAGGCACACTTCGTCGGGTACAGCGACAATGACCACGCCGGCGATATCGACACTAGCAAGAGCA[C/T]
GAATAGGATGCTCTTTTTCCTCAGCGAGTGCCTCGTTAGTTGGCAGTCAGTCAAGCAGCAGGTGGTGGCCTTGTCCAGCTGCGAAGCCGAGTACATAGAG

Reverse complement sequence

CTCTATGTACTCGGCTTCGCAGCTGGACAAGGCCACCACCTGCTGCTTGACTGACTGCCAACTAACGAGGCACTCGCTGAGGAAAAAGAGCATCCTATTC[G/A]
TGCTCTTGCTAGTGTCGATATCGCCGGCGTGGTCATTGTCGCTGTACCCGACGAAGTGTGCCTTTCCAGGACATTTCGGGTAGTAGAGACTGTGGTCGAG

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	95.20%	4.70%	0.11%	0.00%	NA
All Indica	2759	93.70%	6.20%	0.11%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.00%	0.00%	NA
Aus	269	87.40%	12.30%	0.37%	0.00%	NA
Indica I	595	99.80%	0.20%	0.00%	0.00%	NA
Indica II	465	73.80%	25.80%	0.43%	0.00%	NA
Indica III	913	98.50%	1.40%	0.11%	0.00%	NA
Indica Intermediate	786	95.30%	4.70%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.00%	1.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	1.11%	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
vg0220021692	C -> T	LOC_Os02g33630.1	downstream_gene_variant ; 4947.0bp to feature; MODIFIER	silent_mutation	Average:66.437; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N
vg0220021692	C -> T	LOC_Os02g33620.1	intron_variant ; MODIFIER	silent_mutation	Average:66.437; most accessible tissue: Zhenshan97 young leaf, score: 82.077	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220021692	3.92E-06	NA	mr1785	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