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Detailed information for vg0220016136:

Variant ID: vg0220016136 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 20016136
Reference Allele: T	Alternative Allele: C
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 300. )

Flanking Sequence (100 bp) in Reference Genome:

CATCATTGTTCACCCAAACAACTTATTTAAGACCGGGAGGTCGGACATAACATTCACCCAAACAACTTATTTAAGAACAAGAGGTCGGACAAAGCATGCA[T/C]
CGCATGTTCATCACAATTTGCATGCTTAACCTCTGCAGTAATGGAATAAGTGTTGCACTGTTGGTCTTCTTATGCTGCAGATGGAATAAGTGTTGCACTG

Reverse complement sequence

CAGTGCAACACTTATTCCATCTGCAGCATAAGAAGACCAACAGTGCAACACTTATTCCATTACTGCAGAGGTTAAGCATGCAAATTGTGATGAACATGCG[A/G]
TGCATGCTTTGTCCGACCTCTTGTTCTTAAATAAGTTGTTTGGGTGAATGTTATGTCCGACCTCCCGGTCTTAAATAAGTTGTTTGGGTGAACAATGATG

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	91.10%	6.30%	2.58%	0.00%	NA
All Indica	2759	99.00%	0.40%	0.62%	0.00%	NA
All Japonica	1512	74.80%	18.70%	6.48%	0.00%	NA
Aus	269	98.90%	0.00%	1.12%	0.00%	NA
Indica I	595	96.30%	1.30%	2.35%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	99.60%	0.10%	0.25%	0.00%	NA
Temperate Japonica	767	58.00%	34.00%	7.95%	0.00%	NA
Tropical Japonica	504	95.60%	0.80%	3.57%	0.00%	NA
Japonica Intermediate	241	84.60%	7.50%	7.88%	0.00%	NA
VI/Aromatic	96	99.00%	1.00%	0.00%	0.00%	NA
Intermediate	90	88.90%	6.70%	4.44%	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
vg0220016136	T -> C	LOC_Os02g33620.1	upstream_gene_variant ; 957.0bp to feature; MODIFIER	silent_mutation	Average:41.812; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0220016136	T -> C	LOC_Os02g33610.1	downstream_gene_variant ; 2284.0bp to feature; MODIFIER	silent_mutation	Average:41.812; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0220016136	T -> C	LOC_Os02g33610.2	downstream_gene_variant ; 2284.0bp to feature; MODIFIER	silent_mutation	Average:41.812; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N
vg0220016136	T -> C	LOC_Os02g33610-LOC_Os02g33620	intergenic_region ; MODIFIER	silent_mutation	Average:41.812; most accessible tissue: Zhenshan97 young leaf, score: 67.83	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0220016136	4.76E-07	NA	mr1174	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