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Detailed information for vg0608717202:

Variant ID: vg0608717202 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8717202
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTTGTGCCCCTGCTAGTAACCTGGGTACAACGACATTCTGTAGTCCTCTAACATCTTGTCCAATTTATGGGCCCCCTTTTCACTTTCGCAGTCCTCCTTG[G/A]
CGTCCTGCAACATCTGACCAAGATCATCAGCAACGTCGTTACCATCAGCATCCCTTTCCTCCTCACCCGTTTGATTTCCTTCAAATCCAGCGTACTGAGC

Reverse complement sequence

GCTCAGTACGCTGGATTTGAAGGAAATCAAACGGGTGAGGAGGAAAGGGATGCTGATGGTAACGACGTTGCTGATGATCTTGGTCAGATGTTGCAGGACG[C/T]
CAAGGAGGACTGCGAAAGTGAAAAGGGGGCCCATAAATTGGACAAGATGTTAGAGGACTACAGAATGTCGTTGTACCCAGGTTACTAGCAGGGGCACAAA

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.30%	0.60%	0.04%	0.00%	NA
All Indica	2759	98.90%	1.10%	0.07%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	96.50%	3.20%	0.34%	0.00%	NA
Indica II	465	99.40%	0.60%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.10%	0.90%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	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
vg0608717202	G -> A	LOC_Os06g15350.1	missense_variant ; p.Ala48Val; MODERATE	N	Average:17.636; most accessible tissue: Callus, score: 31.397	N	N	N	N
vg0608717202	G -> A	LOC_Os06g15360.1	upstream_gene_variant ; 3356.0bp to feature; MODIFIER	N	Average:17.636; most accessible tissue: Callus, score: 31.397	N	N	N	N
vg0608717202	G -> A	LOC_Os06g15360.2	upstream_gene_variant ; 3356.0bp to feature; MODIFIER	N	Average:17.636; most accessible tissue: Callus, score: 31.397	N	N	N	N
vg0608717202	G -> A	LOC_Os06g15360.4	upstream_gene_variant ; 3378.0bp to feature; MODIFIER	N	Average:17.636; most accessible tissue: Callus, score: 31.397	N	N	N	N
vg0608717202	G -> A	LOC_Os06g15360.3	upstream_gene_variant ; 3807.0bp to feature; MODIFIER	N	Average:17.636; most accessible tissue: Callus, score: 31.397	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608717202	1.80E-06	NA	mr1908	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