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Detailed information for vg0710014852:

Variant ID: vg0710014852 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10014852
Reference Allele: A	Alternative Allele: C,T
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 286. )

Flanking Sequence (100 bp) in Reference Genome:

CGTGCTTAAGATAGAATAAGCATCATCATCATGTAGAGAACGCAATAGCATTGCGACTAACAGAAGTAACAAAAACAGAAATAGCGGTAGAGAGTTATAC[A/C,T]
CTGTGAAAGTCCCTCCGCTGGATTATGTGGCAGAACTGCCTCCGTTGGTATTGTCGATCGGGGCGCCAGCTCCGGCTCCCGCTCCAGGTGTGCCATCTCT

Reverse complement sequence

AGAGATGGCACACCTGGAGCGGGAGCCGGAGCTGGCGCCCCGATCGACAATACCAACGGAGGCAGTTCTGCCACATAATCCAGCGGAGGGACTTTCACAG[T/G,A]
GTATAACTCTCTACCGCTATTTCTGTTTTTGTTACTTCTGTTAGTCGCAATGCTATTGCGTTCTCTACATGATGATGATGCTTATTCTATCTTAAGCACG

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	85.80%	8.80%	4.38%	0.53%	T: 0.55%
All Indica	2759	92.30%	0.90%	5.22%	0.58%	T: 0.94%
All Japonica	1512	72.20%	24.30%	3.44%	0.00%	NA
Aus	269	96.30%	1.50%	2.23%	0.00%	NA
Indica I	595	96.10%	0.80%	2.86%	0.00%	T: 0.17%
Indica II	465	85.80%	1.90%	9.68%	0.43%	T: 2.15%
Indica III	913	93.10%	0.10%	4.60%	1.20%	T: 0.99%
Indica Intermediate	786	92.40%	1.40%	5.09%	0.38%	T: 0.76%
Temperate Japonica	767	60.80%	34.90%	4.30%	0.00%	NA
Tropical Japonica	504	86.70%	10.90%	2.38%	0.00%	NA
Japonica Intermediate	241	78.40%	18.70%	2.90%	0.00%	NA
VI/Aromatic	96	88.50%	1.00%	2.08%	8.33%	NA
Intermediate	90	78.90%	16.70%	3.33%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710014852	A -> DEL	N	N	silent_mutation	Average:34.304; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0710014852	A -> T	LOC_Os07g17010.1	upstream_gene_variant ; 3874.0bp to feature; MODIFIER	silent_mutation	Average:34.304; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0710014852	A -> T	LOC_Os07g17000-LOC_Os07g17010	intergenic_region ; MODIFIER	silent_mutation	Average:34.304; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0710014852	A -> C	LOC_Os07g17010.1	upstream_gene_variant ; 3874.0bp to feature; MODIFIER	silent_mutation	Average:34.304; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N
vg0710014852	A -> C	LOC_Os07g17000-LOC_Os07g17010	intergenic_region ; MODIFIER	silent_mutation	Average:34.304; most accessible tissue: Zhenshan97 young leaf, score: 49.329	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0710014852	2.06E-07	2.73E-08	mr1955	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
vg0710014852	4.76E-06	4.76E-06	mr1955	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