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Detailed information for vg0715830231:

Variant ID: vg0715830231 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 15830231
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.94, G: 0.06, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

CCTGTGGAATGGAGTCGCCCCTCTGCTGAAGTCAAGCTTCCGAGTTTACTTCGTTTTATCTTTTCCGCTGCATTTGTAAACTTTTATATTTTTGTAAGAC[A/G]
TGGATCTGTATGTCAACAATTGTCGTTTGTGTACCCTGGCTAGTCCTGGACAGGGATTTAATGCACATTCAGCTTAGAAATTCTGGTTCGTGAATTTCTG

Reverse complement sequence

CAGAAATTCACGAACCAGAATTTCTAAGCTGAATGTGCATTAAATCCCTGTCCAGGACTAGCCAGGGTACACAAACGACAATTGTTGACATACAGATCCA[T/C]
GTCTTACAAAAATATAAAAGTTTACAAATGCAGCGGAAAAGATAAAACGAAGTAAACTCGGAAGCTTGACTTCAGCAGAGGGGCGACTCCATTCCACAGG

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	36.40%	1.40%	8.63%	53.53%	NA
All Indica	2759	5.40%	2.40%	11.60%	80.65%	NA
All Japonica	1512	93.30%	0.00%	0.13%	6.61%	NA
Aus	269	10.40%	0.00%	31.23%	58.36%	NA
Indica I	595	2.50%	3.20%	11.76%	82.52%	NA
Indica II	465	6.90%	2.20%	7.53%	83.44%	NA
Indica III	913	3.00%	2.10%	13.36%	81.60%	NA
Indica Intermediate	786	9.50%	2.20%	11.83%	76.46%	NA
Temperate Japonica	767	88.50%	0.00%	0.13%	11.34%	NA
Tropical Japonica	504	98.00%	0.00%	0.00%	1.98%	NA
Japonica Intermediate	241	98.30%	0.00%	0.41%	1.24%	NA
VI/Aromatic	96	91.70%	0.00%	0.00%	8.33%	NA
Intermediate	90	52.20%	1.10%	2.22%	44.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0715830231	A -> DEL	N	N	silent_mutation	Average:13.777; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0715830231	A -> G	LOC_Os07g27230.1	upstream_gene_variant ; 2450.0bp to feature; MODIFIER	silent_mutation	Average:13.777; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0715830231	A -> G	LOC_Os07g27240.1	upstream_gene_variant ; 442.0bp to feature; MODIFIER	silent_mutation	Average:13.777; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N
vg0715830231	A -> G	LOC_Os07g27230-LOC_Os07g27240	intergenic_region ; MODIFIER	silent_mutation	Average:13.777; most accessible tissue: Minghui63 panicle, score: 29.741	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0715830231	NA	1.18E-07	mr1915	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
vg0715830231	5.34E-07	NA	mr1613_2	Jap_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