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Detailed information for vg1110039605:

Variant ID: vg1110039605 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10039605
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.51, A: 0.49, others allele: 0.00, population size: 57. )

Flanking Sequence (100 bp) in Reference Genome:

TATCCTATGAGCCCATAATGCTTCTGAAAGCACCTTATGCCACTTCTTTGGGTGTACTTCAAACTTATTTCTGACTAATTTCAACAATGTTTTATTACTC[A/G]
ACTCGGCTTATCCATTAGCCTGAGCGTAGTAAGGAGAAGAACTCAACAACTTAATATCATAAGATTTGGCAAAACTTCTCACCTCTTTTGACATAAAAGA

Reverse complement sequence

TCTTTTATGTCAAAAGAGGTGAGAAGTTTTGCCAAATCTTATGATATTAAGTTGTTGAGTTCTTCTCCTTACTACGCTCAGGCTAATGGATAAGCCGAGT[T/C]
GAGTAATAAAACATTGTTGAAATTAGTCAGAAATAAGTTTGAAGTACACCCAAAGAAGTGGCATAAGGTGCTTTCAGAAGCATTATGGGCTCATAGGATA

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	49.90%	4.00%	0.83%	45.22%	NA
All Indica	2759	29.10%	1.70%	1.30%	67.89%	NA
All Japonica	1512	93.70%	4.20%	0.07%	2.05%	NA
Aus	269	28.30%	0.70%	0.37%	70.63%	NA
Indica I	595	43.90%	5.90%	0.84%	49.41%	NA
Indica II	465	26.20%	0.00%	0.22%	73.55%	NA
Indica III	913	15.40%	0.20%	2.30%	82.04%	NA
Indica Intermediate	786	35.60%	1.10%	1.15%	62.09%	NA
Temperate Japonica	767	93.10%	5.00%	0.00%	1.96%	NA
Tropical Japonica	504	94.00%	3.00%	0.20%	2.78%	NA
Japonica Intermediate	241	95.00%	4.10%	0.00%	0.83%	NA
VI/Aromatic	96	20.80%	70.80%	0.00%	8.33%	NA
Intermediate	90	47.80%	12.20%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110039605	A -> DEL	N	N	silent_mutation	Average:10.898; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1110039605	A -> G	LOC_Os11g17890.1	downstream_gene_variant ; 2524.0bp to feature; MODIFIER	silent_mutation	Average:10.898; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg1110039605	A -> G	LOC_Os11g17900.1	intron_variant ; MODIFIER	silent_mutation	Average:10.898; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110039605	2.69E-06	NA	mr1119	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
vg1110039605	1.77E-07	NA	mr1247	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
vg1110039605	4.03E-06	NA	mr1917	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
vg1110039605	8.44E-06	NA	mr1240_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