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Detailed information for vg1125722116:

Variant ID: vg1125722116 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25722116
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.98, others allele: 0.00, population size: 68. )

Flanking Sequence (100 bp) in Reference Genome:

TCTTCGGCAGGGTCCACCTCCTCGTCTTCGAGAACTGGAGGGGTTAATTATATAGAGCAAGGGTGCGTGCGGGAGTACTCAGCAAGTCAGGGGAATTAAG[T/A]
GTTTGATGCAAGCTTCAAAGGAGAGCCAGTTATTTTTCGCATTCGATCTTAGTTTAAGACTTTCAGAAACAACTAAGTGAGTGCTTCTCAACGACACGGA

Reverse complement sequence

TCCGTGTCGTTGAGAAGCACTCACTTAGTTGTTTCTGAAAGTCTTAAACTAAGATCGAATGCGAAAAATAACTGGCTCTCCTTTGAAGCTTGCATCAAAC[A/T]
CTTAATTCCCCTGACTTGCTGAGTACTCCCGCACGCACCCTTGCTCTATATAATTAACCCCTCCAGTTCTCGAAGACGAGGAGGTGGACCCTGCCGAAGA

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	57.70%	5.30%	2.41%	34.51%	NA
All Indica	2759	60.30%	8.40%	2.94%	28.42%	NA
All Japonica	1512	55.20%	0.40%	1.26%	43.12%	NA
Aus	269	56.10%	4.80%	2.23%	36.80%	NA
Indica I	595	82.00%	1.00%	0.84%	16.13%	NA
Indica II	465	53.30%	24.50%	6.67%	15.48%	NA
Indica III	913	55.60%	2.20%	2.08%	40.09%	NA
Indica Intermediate	786	53.30%	11.60%	3.31%	31.81%	NA
Temperate Japonica	767	73.70%	0.50%	1.30%	24.51%	NA
Tropical Japonica	504	29.80%	0.40%	1.59%	68.25%	NA
Japonica Intermediate	241	49.80%	0.00%	0.41%	49.79%	NA
VI/Aromatic	96	29.20%	1.00%	5.21%	64.58%	NA
Intermediate	90	57.80%	1.10%	3.33%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125722116	T -> A	LOC_Os11g42710.1	upstream_gene_variant ; 1941.0bp to feature; MODIFIER	silent_mutation	Average:13.802; most accessible tissue: Zhenshan97 flag leaf, score: 29.417	N	N	N	N
vg1125722116	T -> A	LOC_Os11g42700.1	downstream_gene_variant ; 324.0bp to feature; MODIFIER	silent_mutation	Average:13.802; most accessible tissue: Zhenshan97 flag leaf, score: 29.417	N	N	N	N
vg1125722116	T -> A	LOC_Os11g42700-LOC_Os11g42710	intergenic_region ; MODIFIER	silent_mutation	Average:13.802; most accessible tissue: Zhenshan97 flag leaf, score: 29.417	N	N	N	N
vg1125722116	T -> DEL	N	N	silent_mutation	Average:13.802; most accessible tissue: Zhenshan97 flag leaf, score: 29.417	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125722116	4.28E-06	4.28E-06	mr1682	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