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Detailed information for vg0806591666:

Variant ID: vg0806591666 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 6591666
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

GTGGCATGTATACATGTATAGTAGGAGTGCTAATAAATACTATACTTGCATATTGAGTATTAGTTGTTTATTGGGTATTAGTTTTATAGAAAGAAGGGAT[A/G]
TCTCAAATACTTCTTACATATTTATATATGGATTTGCTACAAAGATGTCGACACATTTTTTTGTTAATCTCAGTTAGTTTCTGTCCGTTTGATTGCTCCA

Reverse complement sequence

TGGAGCAATCAAACGGACAGAAACTAACTGAGATTAACAAAAAAATGTGTCGACATCTTTGTAGCAAATCCATATATAAATATGTAAGAAGTATTTGAGA[T/C]
ATCCCTTCTTTCTATAAAACTAATACCCAATAAACAACTAATACTCAATATGCAAGTATAGTATTTATTAGCACTCCTACTATACATGTATACATGCCAC

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	32.00%	0.40%	53.70%	13.99%	NA
All Indica	2759	3.50%	0.60%	72.78%	23.09%	NA
All Japonica	1512	90.50%	0.00%	8.66%	0.79%	NA
Aus	269	0.70%	0.00%	97.77%	1.49%	NA
Indica I	595	4.40%	0.00%	54.96%	40.67%	NA
Indica II	465	4.50%	0.40%	76.77%	18.28%	NA
Indica III	913	1.60%	1.20%	81.16%	15.99%	NA
Indica Intermediate	786	4.50%	0.50%	74.17%	20.87%	NA
Temperate Japonica	767	86.40%	0.00%	12.78%	0.78%	NA
Tropical Japonica	504	96.00%	0.00%	3.17%	0.79%	NA
Japonica Intermediate	241	92.10%	0.00%	7.05%	0.83%	NA
VI/Aromatic	96	4.20%	0.00%	93.75%	2.08%	NA
Intermediate	90	42.20%	0.00%	51.11%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0806591666	A -> G	LOC_Os08g11210.1	upstream_gene_variant ; 3837.0bp to feature; MODIFIER	silent_mutation	Average:6.49; most accessible tissue: Minghui63 flag leaf, score: 10.316	N	N	N	N
vg0806591666	A -> G	LOC_Os08g11210-LOC_Os08g11220	intergenic_region ; MODIFIER	silent_mutation	Average:6.49; most accessible tissue: Minghui63 flag leaf, score: 10.316	N	N	N	N
vg0806591666	A -> DEL	N	N	silent_mutation	Average:6.49; most accessible tissue: Minghui63 flag leaf, score: 10.316	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0806591666	NA	2.32E-21	mr1588	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
vg0806591666	2.37E-06	6.70E-30	mr1588_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
vg0806591666	NA	5.03E-09	mr1588_2	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