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Detailed information for vg0818704582:

Variant ID: vg0818704582 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 18704582
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, G: 0.40, others allele: 0.00, population size: 85. )

Flanking Sequence (100 bp) in Reference Genome:

CTTATCTGGGAGATACTTTGGTGCGGGTATAATGTTTGCTTATGCAATTACTCTATGTCATGACGATGATATTACAGTAGTATCTGATAGTTTAGGCGTG[A/G]
TGTCTAGATTACGGGATATCATTATTTGGGGTTATATATTGCGGATGAGAGGTGGGCCGCTGATGGTAACAGCTCAGTACGGGTATTCCTTCGCGCCTAT

Reverse complement sequence

ATAGGCGCGAAGGAATACCCGTACTGAGCTGTTACCATCAGCGGCCCACCTCTCATCCGCAATATATAACCCCAAATAATGATATCCCGTAATCTAGACA[T/C]
CACGCCTAAACTATCAGATACTACTGTAATATCATCGTCATGACATAGAGTAATTGCATAAGCAAACATTATACCCGCACCAAAGTATCTCCCAGATAAG

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	41.00%	40.70%	2.98%	15.34%	NA
All Indica	2759	63.60%	11.40%	4.78%	20.22%	NA
All Japonica	1512	1.50%	87.50%	0.46%	10.58%	NA
Aus	269	48.00%	52.00%	0.00%	0.00%	NA
Indica I	595	76.60%	17.60%	1.34%	4.37%	NA
Indica II	465	86.90%	6.70%	1.72%	4.73%	NA
Indica III	913	51.70%	5.60%	7.23%	35.49%	NA
Indica Intermediate	786	53.80%	16.20%	6.36%	23.66%	NA
Temperate Japonica	767	0.30%	99.00%	0.00%	0.78%	NA
Tropical Japonica	504	3.20%	67.50%	1.19%	28.17%	NA
Japonica Intermediate	241	1.70%	92.90%	0.41%	4.98%	NA
VI/Aromatic	96	6.20%	92.70%	0.00%	1.04%	NA
Intermediate	90	28.90%	62.20%	2.22%	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
vg0818704582	A -> G	LOC_Os08g30410.1	upstream_gene_variant ; 2603.0bp to feature; MODIFIER	silent_mutation	Average:35.531; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0818704582	A -> G	LOC_Os08g30400.1	downstream_gene_variant ; 2290.0bp to feature; MODIFIER	silent_mutation	Average:35.531; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0818704582	A -> G	LOC_Os08g30400-LOC_Os08g30410	intergenic_region ; MODIFIER	silent_mutation	Average:35.531; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N
vg0818704582	A -> DEL	N	N	silent_mutation	Average:35.531; most accessible tissue: Zhenshan97 flag leaf, score: 54.545	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0818704582	4.08E-06	NA	mr1540	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
vg0818704582	NA	3.49E-07	mr1639	Jap_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
vg0818704582	NA	2.89E-06	mr1929_2	Jap_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