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Detailed information for vg0223196089:

Variant ID: vg0223196089 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 23196089
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

TCGACTGCCACAACCGCATATCCACCTCATGCGCCGCAAGCGGGCGAATGGGATTAGTGGAAGCGTGGGCACGAGAAACAAGGGAGCGAGATAGTGAGAA[A/G]
CGAGGGAGCGAAATAGTGGGCGCGAGAAACGAGGAGCCGGGCTCATCGATGGCAAGGGTATAAAGATACCGAGGAAAAGATTTGCTCCCTTCCTTTCGCC

Reverse complement sequence

GGCGAAAGGAAGGGAGCAAATCTTTTCCTCGGTATCTTTATACCCTTGCCATCGATGAGCCCGGCTCCTCGTTTCTCGCGCCCACTATTTCGCTCCCTCG[T/C]
TTCTCACTATCTCGCTCCCTTGTTTCTCGTGCCCACGCTTCCACTAATCCCATTCGCCCGCTTGCGGCGCATGAGGTGGATATGCGGTTGTGGCAGTCGA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	44.40%	12.20%	42.19%	1.27%	NA
All Indica	2759	20.60%	19.20%	59.91%	0.22%	NA
All Japonica	1512	88.20%	0.50%	7.87%	3.37%	NA
Aus	269	35.30%	4.50%	59.11%	1.12%	NA
Indica I	595	22.90%	14.10%	62.52%	0.50%	NA
Indica II	465	20.60%	19.80%	59.57%	0.00%	NA
Indica III	913	13.40%	22.90%	63.64%	0.11%	NA
Indica Intermediate	786	27.40%	18.60%	53.82%	0.25%	NA
Temperate Japonica	767	90.60%	0.30%	5.61%	3.52%	NA
Tropical Japonica	504	90.70%	1.20%	7.54%	0.60%	NA
Japonica Intermediate	241	75.50%	0.00%	15.77%	8.71%	NA
VI/Aromatic	96	40.60%	16.70%	42.71%	0.00%	NA
Intermediate	90	65.60%	10.00%	24.44%	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
vg0223196089	A -> G	LOC_Os02g38370.1	upstream_gene_variant ; 202.0bp to feature; MODIFIER	silent_mutation	Average:78.321; most accessible tissue: Zhenshan97 flag leaf, score: 93.632	N	N	N	N
vg0223196089	A -> G	LOC_Os02g38380.1	downstream_gene_variant ; 4304.0bp to feature; MODIFIER	silent_mutation	Average:78.321; most accessible tissue: Zhenshan97 flag leaf, score: 93.632	N	N	N	N
vg0223196089	A -> G	LOC_Os02g38350-LOC_Os02g38370	intergenic_region ; MODIFIER	silent_mutation	Average:78.321; most accessible tissue: Zhenshan97 flag leaf, score: 93.632	N	N	N	N
vg0223196089	A -> DEL	N	N	silent_mutation	Average:78.321; most accessible tissue: Zhenshan97 flag leaf, score: 93.632	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0223196089	3.79E-06	8.58E-06	mr1018	Ind_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
vg0223196089	3.30E-06	4.16E-06	mr1334	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