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Detailed information for vg0710603879:

Variant ID: vg0710603879 (JBrowse)	Variation Type: SNP
Chromosome: chr07	Position: 10603879
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.99, G: 0.02, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

CCATCCATGCTTTAAATTTAGAAAATTTTATTTCCCACATTTAACTTCACTTGTAAATTAAAGAACATTTAATATAAATTCTAATAATAATTTATTAAAT[G/A]
ATTTATAAATCCTGAAACAAAAATCAGGATGTGACAGATCTACCCCCCTTACAAAGAATCTCGTCCCGAGATTCGGAACGGCTAGAAAGAAAAAGGGAAT

Reverse complement sequence

ATTCCCTTTTTCTTTCTAGCCGTTCCGAATCTCGGGACGAGATTCTTTGTAAGGGGGGTAGATCTGTCACATCCTGATTTTTGTTTCAGGATTTATAAAT[C/T]
ATTTAATAAATTATTATTAGAATTTATATTAAATGTTCTTTAATTTACAAGTGAAGTTAAATGTGGGAAATAAAATTTTCTAAATTTAAAGCATGGATGG

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	34.40%	0.80%	5.99%	58.78%	NA
All Indica	2759	4.40%	0.60%	5.00%	90.00%	NA
All Japonica	1512	88.10%	0.10%	1.06%	10.78%	NA
Aus	269	49.80%	5.60%	18.59%	26.02%	NA
Indica I	595	1.70%	0.20%	1.85%	96.30%	NA
Indica II	465	4.30%	0.20%	3.01%	92.47%	NA
Indica III	913	1.00%	1.10%	8.87%	89.05%	NA
Indica Intermediate	786	10.40%	0.60%	4.07%	84.86%	NA
Temperate Japonica	767	86.60%	0.00%	0.78%	12.65%	NA
Tropical Japonica	504	86.50%	0.20%	1.19%	12.10%	NA
Japonica Intermediate	241	96.30%	0.00%	1.66%	2.07%	NA
VI/Aromatic	96	5.20%	5.20%	73.96%	15.62%	NA
Intermediate	90	37.80%	1.10%	8.89%	52.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0710603879	G -> DEL	N	N	silent_mutation	Average:10.705; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0710603879	G -> A	LOC_Os07g17910.1	upstream_gene_variant ; 3776.0bp to feature; MODIFIER	silent_mutation	Average:10.705; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0710603879	G -> A	LOC_Os07g17930.1	upstream_gene_variant ; 4099.0bp to feature; MODIFIER	silent_mutation	Average:10.705; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0710603879	G -> A	LOC_Os07g17920.1	downstream_gene_variant ; 481.0bp to feature; MODIFIER	silent_mutation	Average:10.705; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0710603879	G -> A	LOC_Os07g17910-LOC_Os07g17920	intergenic_region ; MODIFIER	silent_mutation	Average:10.705; 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
vg0710603879	NA	3.26E-26	mr1181	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
vg0710603879	NA	1.66E-32	mr1213	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
vg0710603879	NA	4.95E-12	mr1329	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
vg0710603879	NA	2.10E-07	mr1559	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
vg0710603879	NA	2.67E-21	mr1698	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
vg0710603879	5.85E-07	8.25E-07	mr1698	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
vg0710603879	NA	1.22E-06	mr1761	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
vg0710603879	NA	7.65E-39	mr1152_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
vg0710603879	NA	6.83E-09	mr1198_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
vg0710603879	NA	1.42E-06	mr1275_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
vg0710603879	NA	1.97E-21	mr1298_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
vg0710603879	NA	3.52E-14	mr1575_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
vg0710603879	NA	2.04E-25	mr1698_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
vg0710603879	NA	5.38E-20	mr1731_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
vg0710603879	NA	5.95E-15	mr1767_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
vg0710603879	NA	1.18E-07	mr1909_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
vg0710603879	NA	1.86E-08	mr1940_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
vg0710603879	NA	7.29E-14	mr1950_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