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Detailed information for vg0820443724:

Variant ID: vg0820443724 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 20443724
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.61, G: 0.39, others allele: 0.00, population size: 76. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGATCTTAATCAAATTTCTCTATCTCGGTCTTTTTTTTCTATTGGTTTTAGTCTTTTTTTTCCTTCACCCCTATTGGCACGATGGTAATGCTCTACTG[A/G]
CCGATTTTGCAAAACAACACGTGAGTATCCACCTAGTAAGAATGGATCAAGCTGAGTGTTTATTAGATTATTTTTTGGACTGTGTACTACTGTATTTTAC

Reverse complement sequence

GTAAAATACAGTAGTACACAGTCCAAAAAATAATCTAATAAACACTCAGCTTGATCCATTCTTACTAGGTGGATACTCACGTGTTGTTTTGCAAAATCGG[T/C]
CAGTAGAGCATTACCATCGTGCCAATAGGGGTGAAGGAAAAAAAAGACTAAAACCAATAGAAAAAAAAGACCGAGATAGAGAAATTTGATTAAGATCCAA

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	66.00%	24.20%	0.15%	9.65%	NA
All Indica	2759	75.10%	8.40%	0.14%	16.35%	NA
All Japonica	1512	44.00%	55.80%	0.20%	0.07%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.00%	1.30%	0.34%	1.34%	NA
Indica II	465	84.50%	12.30%	0.00%	3.23%	NA
Indica III	913	56.40%	10.00%	0.00%	33.63%	NA
Indica Intermediate	786	74.70%	9.70%	0.25%	15.39%	NA
Temperate Japonica	767	27.00%	72.90%	0.13%	0.00%	NA
Tropical Japonica	504	68.80%	30.60%	0.40%	0.20%	NA
Japonica Intermediate	241	46.10%	53.90%	0.00%	0.00%	NA
VI/Aromatic	96	59.40%	40.60%	0.00%	0.00%	NA
Intermediate	90	60.00%	35.60%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0820443724	A -> G	LOC_Os08g32950.1	upstream_gene_variant ; 2834.0bp to feature; MODIFIER	silent_mutation	Average:56.965; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N
vg0820443724	A -> G	LOC_Os08g32940-LOC_Os08g32950	intergenic_region ; MODIFIER	silent_mutation	Average:56.965; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N
vg0820443724	A -> DEL	N	N	silent_mutation	Average:56.965; most accessible tissue: Minghui63 panicle, score: 86.012	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0820443724	2.70E-07	2.58E-09	mr1622_2	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