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Detailed information for vg0922141898:

Variant ID: vg0922141898 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 22141898
Reference Allele: T	Alternative Allele: A,C
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.78, A: 0.23, others allele: 0.00, population size: 82. )

Flanking Sequence (100 bp) in Reference Genome:

ATGTTTGTGGAGTGATATATCACATGTTAATACATCTTCTCAATTTTTTTTAATTTTTTTAAAACAATTTGATTAATATGCAAATAATGAGGGGATATCC[T/A,C]
CTCAAGGATCAAAATCCACTCCCGTTGACCGTTGTGATAGCTGATATATTGTGTGTGGCTGCTGCTTTAGTGCTAGCTAGACAAGTTGAGGCCGTAATTA

Reverse complement sequence

TAATTACGGCCTCAACTTGTCTAGCTAGCACTAAAGCAGCAGCCACACACAATATATCAGCTATCACAACGGTCAACGGGAGTGGATTTTGATCCTTGAG[A/T,G]
GGATATCCCCTCATTATTTGCATATTAATCAAATTGTTTTAAAAAAATTAAAAAAAATTGAGAAGATGTATTAACATGTGATATATCACTCCACAAACAT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	38.60%	20.20%	2.01%	39.23%	C: 0.02%
All Indica	2759	3.30%	30.10%	3.01%	63.54%	C: 0.04%
All Japonica	1512	99.50%	0.30%	0.00%	0.20%	NA
Aus	269	25.30%	41.30%	4.09%	29.37%	NA
Indica I	595	1.20%	41.50%	1.85%	55.46%	NA
Indica II	465	6.70%	12.00%	6.24%	75.05%	NA
Indica III	913	1.00%	32.90%	1.97%	64.07%	C: 0.11%
Indica Intermediate	786	5.60%	29.00%	3.18%	62.21%	NA
Temperate Japonica	767	99.70%	0.00%	0.00%	0.26%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	95.80%	1.00%	0.00%	3.12%	NA
Intermediate	90	73.30%	7.80%	1.11%	17.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0922141898	T -> DEL	N	N	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> C	LOC_Os09g38450.1	upstream_gene_variant ; 4857.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> C	LOC_Os09g38480.1	upstream_gene_variant ; 3806.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> C	LOC_Os09g38460.1	downstream_gene_variant ; 2303.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> C	LOC_Os09g38470.1	intron_variant ; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> A	LOC_Os09g38450.1	upstream_gene_variant ; 4857.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> A	LOC_Os09g38480.1	upstream_gene_variant ; 3806.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> A	LOC_Os09g38460.1	downstream_gene_variant ; 2303.0bp to feature; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N
vg0922141898	T -> A	LOC_Os09g38470.1	intron_variant ; MODIFIER	silent_mutation	Average:12.809; most accessible tissue: Callus, score: 89.556	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0922141898	1.44E-06	NA	mr1865	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
vg0922141898	3.86E-06	NA	mr1865	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