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Detailed information for vg0422820213:

Variant ID: vg0422820213 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 22820213
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAAACTAACTAAAATTTGGAATAAATATAATAAAATTAAAAGTAGAGTTTAGAGTATGTATAAAAATACAATTTACAAATAACTAAAATTCGAAATTCGA[A/G]
ATTAAGAATAACATGGGAAGAAGAGTTTAAGGTCAATATAGGAATACAAATATAGAAATACAATTTAGAAGTAACTGAAATTCGAAATTAAAATTAAAGA

Reverse complement sequence

TCTTTAATTTTAATTTCGAATTTCAGTTACTTCTAAATTGTATTTCTATATTTGTATTCCTATATTGACCTTAAACTCTTCTTCCCATGTTATTCTTAAT[T/C]
TCGAATTTCGAATTTTAGTTATTTGTAAATTGTATTTTTATACATACTCTAAACTCTACTTTTAATTTTATTATATTTATTCCAAATTTTAGTTAGTTTT

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	94.90%	2.90%	2.24%	0.00%	NA
All Indica	2759	98.90%	0.40%	0.69%	0.00%	NA
All Japonica	1512	88.00%	6.80%	5.16%	0.00%	NA
Aus	269	95.90%	3.70%	0.37%	0.00%	NA
Indica I	595	98.20%	0.00%	1.85%	0.00%	NA
Indica II	465	99.60%	0.00%	0.43%	0.00%	NA
Indica III	913	99.70%	0.30%	0.00%	0.00%	NA
Indica Intermediate	786	98.30%	0.90%	0.76%	0.00%	NA
Temperate Japonica	767	84.10%	11.10%	4.82%	0.00%	NA
Tropical Japonica	504	92.90%	2.00%	5.16%	0.00%	NA
Japonica Intermediate	241	90.50%	3.30%	6.22%	0.00%	NA
VI/Aromatic	96	84.40%	11.50%	4.17%	0.00%	NA
Intermediate	90	92.20%	3.30%	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
vg0422820213	A -> G	LOC_Os04g38360.1	upstream_gene_variant ; 817.0bp to feature; MODIFIER	silent_mutation	Average:16.875; most accessible tissue: Zhenshan97 flower, score: 24.143	N	N	N	N
vg0422820213	A -> G	LOC_Os04g38370.1	upstream_gene_variant ; 2055.0bp to feature; MODIFIER	silent_mutation	Average:16.875; most accessible tissue: Zhenshan97 flower, score: 24.143	N	N	N	N
vg0422820213	A -> G	LOC_Os04g38350-LOC_Os04g38360	intergenic_region ; MODIFIER	silent_mutation	Average:16.875; most accessible tissue: Zhenshan97 flower, score: 24.143	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0422820213	4.31E-06	NA	mr1403_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
vg0422820213	NA	3.86E-06	mr1403_2	Jap_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