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Detailed information for vg0208038463:

Variant ID: vg0208038463 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 8038463
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACCAGCGTTTGACCATTCATTTTATTCAAATTTTTTGTGCAAATATGAAAATATTTATATCATGCTTAAAGAACATTTGATGATGAATCAAGTCACAAT[A/G]
AAATAAATGATAATTACATAAATTTTTTAAATAATACGAATGATCAAACGTTGGATAAAAAATCAACGGCGTCATACATTAAAATATGGAGGTAGTACTA

Reverse complement sequence

TAGTACTACCTCCATATTTTAATGTATGACGCCGTTGATTTTTTATCCAACGTTTGATCATTCGTATTATTTAAAAAATTTATGTAATTATCATTTATTT[T/C]
ATTGTGACTTGATTCATCATCAAATGTTCTTTAAGCATGATATAAATATTTTCATATTTGCACAAAAAATTTGAATAAAATGAATGGTCAAACGCTGGTT

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	51.40%	0.10%	0.15%	48.31%	NA
All Indica	2759	30.70%	0.20%	0.18%	68.94%	NA
All Japonica	1512	98.00%	0.00%	0.00%	1.98%	NA
Aus	269	4.10%	0.00%	0.74%	95.17%	NA
Indica I	595	36.50%	0.00%	0.34%	63.19%	NA
Indica II	465	17.00%	0.40%	0.00%	82.58%	NA
Indica III	913	34.80%	0.00%	0.22%	64.95%	NA
Indica Intermediate	786	29.60%	0.40%	0.13%	69.85%	NA
Temperate Japonica	767	98.40%	0.00%	0.00%	1.56%	NA
Tropical Japonica	504	97.80%	0.00%	0.00%	2.18%	NA
Japonica Intermediate	241	97.10%	0.00%	0.00%	2.90%	NA
VI/Aromatic	96	44.80%	0.00%	0.00%	55.21%	NA
Intermediate	90	53.30%	0.00%	0.00%	46.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0208038463	A -> G	LOC_Os02g14570.1	upstream_gene_variant ; 3006.0bp to feature; MODIFIER	silent_mutation	Average:42.22; most accessible tissue: Zhenshan97 root, score: 87.466	N	N	N	N
vg0208038463	A -> G	LOC_Os02g14580.1	upstream_gene_variant ; 2650.0bp to feature; MODIFIER	silent_mutation	Average:42.22; most accessible tissue: Zhenshan97 root, score: 87.466	N	N	N	N
vg0208038463	A -> G	LOC_Os02g14570-LOC_Os02g14580	intergenic_region ; MODIFIER	silent_mutation	Average:42.22; most accessible tissue: Zhenshan97 root, score: 87.466	N	N	N	N
vg0208038463	A -> DEL	N	N	silent_mutation	Average:42.22; most accessible tissue: Zhenshan97 root, score: 87.466	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0208038463	6.54E-06	6.54E-06	mr1275	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
vg0208038463	2.60E-06	2.60E-06	mr1770	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
vg0208038463	3.79E-06	3.79E-06	mr1876	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