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Detailed information for vg0620355678:

Variant ID: vg0620355678 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 20355678
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCAAATTTGTGTGACTTGTGTTAGATATCTTTCATACAACATATTTCACTTTTCCCCTTGTCAAATTTGTGCAAAGAAAATATAGCCATGCCCCTTCCAT[A/G]
ATCATGCCAAGAGAACCAATTGGAGAGAAAGTATAGGAAAAAGGGAGAATCATTTCTTTATTCCACCATTCCACAACATATTTCACTTTTCCACTTTTCA

Reverse complement sequence

TGAAAAGTGGAAAAGTGAAATATGTTGTGGAATGGTGGAATAAAGAAATGATTCTCCCTTTTTCCTATACTTTCTCTCCAATTGGTTCTCTTGGCATGAT[T/C]
ATGGAAGGGGCATGGCTATATTTTCTTTGCACAAATTTGACAAGGGGAAAAGTGAAATATGTTGTATGAAAGATATCTAACACAAGTCACACAAATTTGA

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	90.30%	0.80%	4.00%	4.85%	NA
All Indica	2759	92.20%	1.40%	5.91%	0.54%	NA
All Japonica	1512	96.70%	0.00%	0.20%	3.11%	NA
Aus	269	35.70%	0.00%	6.69%	57.62%	NA
Indica I	595	88.60%	1.30%	10.08%	0.00%	NA
Indica II	465	89.90%	2.60%	6.67%	0.86%	NA
Indica III	913	95.90%	0.90%	2.52%	0.66%	NA
Indica Intermediate	786	91.90%	1.30%	6.23%	0.64%	NA
Temperate Japonica	767	96.20%	0.00%	0.39%	3.39%	NA
Tropical Japonica	504	98.00%	0.00%	0.00%	1.98%	NA
Japonica Intermediate	241	95.40%	0.00%	0.00%	4.56%	NA
VI/Aromatic	96	87.50%	2.10%	1.04%	9.38%	NA
Intermediate	90	92.20%	0.00%	4.44%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0620355678	A -> G	LOC_Os06g35000.1	downstream_gene_variant ; 2339.0bp to feature; MODIFIER	silent_mutation	Average:12.345; most accessible tissue: Callus, score: 35.87	N	N	N	N
vg0620355678	A -> G	LOC_Os06g35000-LOC_Os06g35010	intergenic_region ; MODIFIER	silent_mutation	Average:12.345; most accessible tissue: Callus, score: 35.87	N	N	N	N
vg0620355678	A -> DEL	N	N	silent_mutation	Average:12.345; most accessible tissue: Callus, score: 35.87	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0620355678	7.43E-07	7.43E-07	mr1848	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