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Detailed information for vg0906198689:

Variant ID: vg0906198689 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6198689
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.89, A: 0.11, others allele: 0.00, population size: 65. )

Flanking Sequence (100 bp) in Reference Genome:

AATATTTTCGATCTACTTAGTGAAACAATTCCGATATACCTAGTGGAACATCGTGCAACATTTAAAAATAATTCAATAATAAGCTAAAAAAAATTTCGTC[G/A]
GAATATATCAATGCGTGGTCTTGTTTTGAAGATTTAATTACAACGAATTTAATGATGCAATCGGATCATAATTTGAATCAGAATAAGTAATTTAAGAGAA

Reverse complement sequence

TTCTCTTAAATTACTTATTCTGATTCAAATTATGATCCGATTGCATCATTAAATTCGTTGTAATTAAATCTTCAAAACAAGACCACGCATTGATATATTC[C/T]
GACGAAATTTTTTTTAGCTTATTATTGAATTATTTTTAAATGTTGCACGATGTTCCACTAGGTATATCGGAATTGTTTCACTAAGTAGATCGAAAATATT

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	35.70%	35.30%	0.36%	28.65%	NA
All Indica	2759	14.60%	55.50%	0.33%	29.61%	NA
All Japonica	1512	77.70%	0.60%	0.33%	21.36%	NA
Aus	269	19.30%	38.30%	0.00%	42.38%	NA
Indica I	595	23.70%	72.10%	0.17%	4.03%	NA
Indica II	465	9.50%	32.70%	0.22%	57.63%	NA
Indica III	913	9.10%	62.80%	0.00%	28.15%	NA
Indica Intermediate	786	17.20%	47.80%	0.89%	34.10%	NA
Temperate Japonica	767	88.50%	0.30%	0.26%	10.95%	NA
Tropical Japonica	504	76.60%	0.60%	0.40%	22.42%	NA
Japonica Intermediate	241	45.60%	1.70%	0.41%	52.28%	NA
VI/Aromatic	96	11.50%	6.20%	1.04%	81.25%	NA
Intermediate	90	51.10%	22.20%	2.22%	24.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0906198689	G -> DEL	N	N	silent_mutation	Average:18.775; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0906198689	G -> A	LOC_Os09g11170.1	downstream_gene_variant ; 1772.0bp to feature; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0906198689	G -> A	LOC_Os09g11180.1	downstream_gene_variant ; 858.0bp to feature; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N
vg0906198689	G -> A	LOC_Os09g11180-LOC_Os09g11190	intergenic_region ; MODIFIER	silent_mutation	Average:18.775; most accessible tissue: Zhenshan97 panicle, score: 43.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906198689	1.49E-06	1.49E-06	mr1321	Ind_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
vg0906198689	NA	5.45E-08	mr1439	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
vg0906198689	NA	3.66E-06	mr1511	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
vg0906198689	NA	2.39E-06	mr1881	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
vg0906198689	NA	3.37E-06	mr1137_2	Ind_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
vg0906198689	NA	9.42E-06	mr1348_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
vg0906198689	NA	8.11E-06	mr1617_2	Ind_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