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Detailed information for vg0907441318:

Variant ID: vg0907441318 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 7441318
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.54, G: 0.47, others allele: 0.00, population size: 94. )

Flanking Sequence (100 bp) in Reference Genome:

CCCCCGAATGTGCGGTTTCAAGTTGACCGATCATGGCACGAGGACTTCAACAGTGCCTGGAGTGGAGCTGGCCGGACCGAGTACGGCAGCGCATATTTGA[T/G]
ATCTAGTCTAGCCTGATAGAGGTGTTTTGCTTGAAACCTCGGGACTTTGGCAATACTTGGGCACGGTCCAAGTTCCAAACTCTGTTAACACCAAAATTTG

Reverse complement sequence

CAAATTTTGGTGTTAACAGAGTTTGGAACTTGGACCGTGCCCAAGTATTGCCAAAGTCCCGAGGTTTCAAGCAAAACACCTCTATCAGGCTAGACTAGAT[A/C]
TCAAATATGCGCTGCCGTACTCGGTCCGGCCAGCTCCACTCCAGGCACTGTTGAAGTCCTCGTGCCATGATCGGTCAACTTGAAACCGCACATTCGGGGG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	71.80%	27.10%	0.21%	0.87%	NA
All Indica	2759	58.20%	40.50%	0.36%	0.94%	NA
All Japonica	1512	99.20%	0.80%	0.00%	0.00%	NA
Aus	269	45.70%	50.20%	0.00%	4.09%	NA
Indica I	595	78.50%	20.80%	0.67%	0.00%	NA
Indica II	465	26.50%	70.50%	0.43%	2.58%	NA
Indica III	913	60.00%	38.70%	0.11%	1.20%	NA
Indica Intermediate	786	59.50%	39.70%	0.38%	0.38%	NA
Temperate Japonica	767	99.50%	0.50%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.70%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	76.70%	18.90%	0.00%	4.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0907441318	T -> G	LOC_Os09g12920.1	upstream_gene_variant ; 3177.0bp to feature; MODIFIER	silent_mutation	Average:60.528; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg0907441318	T -> G	LOC_Os09g12910.1	downstream_gene_variant ; 1632.0bp to feature; MODIFIER	silent_mutation	Average:60.528; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg0907441318	T -> G	LOC_Os09g12910-LOC_Os09g12920	intergenic_region ; MODIFIER	silent_mutation	Average:60.528; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N
vg0907441318	T -> DEL	N	N	silent_mutation	Average:60.528; most accessible tissue: Zhenshan97 young leaf, score: 77.101	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0907441318	NA	2.12E-07	mr1190	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
vg0907441318	NA	2.89E-06	mr1445	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