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Detailed information for vg0906656639:

Variant ID: vg0906656639 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 6656639
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGAATAATCCCAATACATAATCTGTCAGCCATTTTAGCCTTCTCTAATACAAGCGCACGGTCGAGGACACCAGCACACTTTACGAAGATCAACTAACA[A/G]
ATTTAGCTCACACGACTGTTCTGCAACTAATATTAAGGAATACCATCAGAGGGTGTGAGAATAACTACGTACAGGTTCCGTTTTGCCTTCCATTCCCATT

Reverse complement sequence

AATGGGAATGGAAGGCAAAACGGAACCTGTACGTAGTTATTCTCACACCCTCTGATGGTATTCCTTAATATTAGTTGCAGAACAGTCGTGTGAGCTAAAT[T/C]
TGTTAGTTGATCTTCGTAAAGTGTGCTGGTGTCCTCGACCGTGCGCTTGTATTAGAGAAGGCTAAAATGGCTGACAGATTATGTATTGGGATTATTCTGG

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	55.00%	41.60%	0.68%	2.71%	NA
All Indica	2759	82.90%	14.80%	0.47%	1.85%	NA
All Japonica	1512	2.70%	97.20%	0.00%	0.07%	NA
Aus	269	63.60%	3.30%	6.32%	26.77%	NA
Indica I	595	95.30%	3.70%	0.84%	0.17%	NA
Indica II	465	63.90%	35.70%	0.43%	0.00%	NA
Indica III	913	91.00%	6.70%	0.33%	1.97%	NA
Indica Intermediate	786	75.40%	20.10%	0.38%	4.07%	NA
Temperate Japonica	767	2.10%	97.90%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	7.50%	92.10%	0.00%	0.41%	NA
VI/Aromatic	96	64.60%	32.30%	0.00%	3.12%	NA
Intermediate	90	42.20%	54.40%	2.22%	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
vg0906656639	A -> G	LOC_Os09g11870.1	upstream_gene_variant ; 67.0bp to feature; MODIFIER	silent_mutation	Average:61.194; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg0906656639	A -> G	LOC_Os09g11870-LOC_Os09g11880	intergenic_region ; MODIFIER	silent_mutation	Average:61.194; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg0906656639	A -> DEL	N	N	silent_mutation	Average:61.194; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0906656639	NA	6.16E-06	mr1057	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
vg0906656639	NA	1.53E-06	mr1245	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
vg0906656639	1.20E-07	1.20E-07	mr1389	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
vg0906656639	2.05E-07	4.76E-09	mr1038_2	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
vg0906656639	NA	6.11E-07	mr1057_2	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
vg0906656639	1.12E-06	1.12E-06	mr1389_2	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