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Detailed information for vg0518708516:

Variant ID: vg0518708516 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 18708516
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.68, G: 0.32, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CGGGTCCCACAATTTTTTAATTAAAAAAACGCTGACTGGATTGCCACGTGTGCGCTACGTTGGACAAAACCGCTTTGAATTGGTTCGAGGGGGGTAATTC[A/G]
TCCGGTTTGTATAGTTGGAGGTGAAGAATGTCCGGTTTTGTGGTTCAGGGGGGTAATTCGGACGACCGCGATAGTTCGGGGGGTAATTCGTACTTTTTCC

Reverse complement sequence

GGAAAAAGTACGAATTACCCCCCGAACTATCGCGGTCGTCCGAATTACCCCCCTGAACCACAAAACCGGACATTCTTCACCTCCAACTATACAAACCGGA[T/C]
GAATTACCCCCCTCGAACCAATTCAAAGCGGTTTTGTCCAACGTAGCGCACACGTGGCAATCCAGTCAGCGTTTTTTTAATTAAAAAATTGTGGGACCCG

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	54.20%	35.10%	5.71%	5.01%	NA
All Indica	2759	81.70%	2.00%	8.48%	7.76%	NA
All Japonica	1512	2.40%	96.50%	0.46%	0.66%	NA
Aus	269	83.30%	4.50%	8.55%	3.72%	NA
Indica I	595	80.30%	1.00%	9.92%	8.74%	NA
Indica II	465	74.60%	3.90%	10.75%	10.75%	NA
Indica III	913	90.30%	1.20%	3.61%	4.93%	NA
Indica Intermediate	786	77.10%	2.70%	11.70%	8.52%	NA
Temperate Japonica	767	2.10%	96.30%	0.65%	0.91%	NA
Tropical Japonica	504	3.40%	95.80%	0.20%	0.60%	NA
Japonica Intermediate	241	1.20%	98.30%	0.41%	0.00%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	45.60%	44.40%	6.67%	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
vg0518708516	A -> DEL	N	N	silent_mutation	Average:49.981; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0518708516	A -> G	LOC_Os05g32090.1	downstream_gene_variant ; 2123.0bp to feature; MODIFIER	silent_mutation	Average:49.981; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N
vg0518708516	A -> G	LOC_Os05g32080-LOC_Os05g32090	intergenic_region ; MODIFIER	silent_mutation	Average:49.981; most accessible tissue: Minghui63 panicle, score: 70.194	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0518708516	1.66E-06	NA	mr1187_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
vg0518708516	NA	3.50E-08	mr1600_2	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