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Detailed information for vg0819321720:

Variant ID: vg0819321720 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 19321720
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACTGAGAGATACATTGGGAATGTATCCTATAGACGCAAGTTTTCATACCGTATACATCAACTAACAAATATCACTAAAAATTTTAGAAAACTTTGTACAT[G/A]
TACTTTCAATAGTATTATATCTACATATAAAGTCACACCTTTAAATTTATTTTACATAAAGAGCAATAAAAAAGATAAAATTAAGATAGACTTGTAGTCT

Reverse complement sequence

AGACTACAAGTCTATCTTAATTTTATCTTTTTTATTGCTCTTTATGTAAAATAAATTTAAAGGTGTGACTTTATATGTAGATATAATACTATTGAAAGTA[C/T]
ATGTACAAAGTTTTCTAAAATTTTTAGTGATATTTGTTAGTTGATGTATACGGTATGAAAACTTGCGTCTATAGGATACATTCCCAATGTATCTCTCAGT

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	68.90%	27.80%	0.06%	3.22%	NA
All Indica	2759	90.80%	3.70%	0.04%	5.47%	NA
All Japonica	1512	28.00%	71.90%	0.07%	0.00%	NA
Aus	269	85.50%	14.50%	0.00%	0.00%	NA
Indica I	595	78.50%	1.00%	0.17%	20.34%	NA
Indica II	465	96.30%	1.10%	0.00%	2.58%	NA
Indica III	913	91.70%	8.30%	0.00%	0.00%	NA
Indica Intermediate	786	95.70%	2.00%	0.00%	2.29%	NA
Temperate Japonica	767	24.90%	75.00%	0.13%	0.00%	NA
Tropical Japonica	504	36.50%	63.50%	0.00%	0.00%	NA
Japonica Intermediate	241	20.30%	79.70%	0.00%	0.00%	NA
VI/Aromatic	96	53.10%	46.90%	0.00%	0.00%	NA
Intermediate	90	51.10%	46.70%	1.11%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0819321720	G -> A	LOC_Os08g31250.1	upstream_gene_variant ; 3416.0bp to feature; MODIFIER	silent_mutation	Average:37.255; most accessible tissue: Callus, score: 79.813	N	N	N	N
vg0819321720	G -> A	LOC_Os08g31240.1	downstream_gene_variant ; 3489.0bp to feature; MODIFIER	silent_mutation	Average:37.255; most accessible tissue: Callus, score: 79.813	N	N	N	N
vg0819321720	G -> A	LOC_Os08g31240-LOC_Os08g31250	intergenic_region ; MODIFIER	silent_mutation	Average:37.255; most accessible tissue: Callus, score: 79.813	N	N	N	N
vg0819321720	G -> DEL	N	N	silent_mutation	Average:37.255; most accessible tissue: Callus, score: 79.813	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0819321720	NA	1.70E-06	mr1622	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
vg0819321720	1.97E-06	3.87E-06	mr1732	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