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Detailed information for vg1117177660:

Variant ID: vg1117177660 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 17177660
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, A: 0.02, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CCAGTTCGGTCGCCAACTTCGTTCAATGCCATTGCCAGGATCTATATATCAAACCGAATTAAACTCAAAACACAAGTTTTAATTATTAGTACTATGATCT[T/A]
AACATGGCAAGTAAGCTATCATGTTTAACTATCTTAACTAATTACACCGGCATCCGTGTATACATGTGACGTCCAACATAACCATCTGTGATGTACTAGC

Reverse complement sequence

GCTAGTACATCACAGATGGTTATGTTGGACGTCACATGTATACACGGATGCCGGTGTAATTAGTTAAGATAGTTAAACATGATAGCTTACTTGCCATGTT[A/T]
AGATCATAGTACTAATAATTAAAACTTGTGTTTTGAGTTTAATTCGGTTTGATATATAGATCCTGGCAATGGCATTGAACGAAGTTGGCGACCGAACTGG

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	80.60%	19.40%	0.06%	0.00%	NA
All Indica	2759	74.20%	25.70%	0.11%	0.00%	NA
All Japonica	1512	99.10%	0.90%	0.00%	0.00%	NA
Aus	269	34.90%	65.10%	0.00%	0.00%	NA
Indica I	595	98.30%	1.50%	0.17%	0.00%	NA
Indica II	465	46.00%	54.00%	0.00%	0.00%	NA
Indica III	913	76.30%	23.70%	0.00%	0.00%	NA
Indica Intermediate	786	70.20%	29.50%	0.25%	0.00%	NA
Temperate Japonica	767	99.20%	0.80%	0.00%	0.00%	NA
Tropical Japonica	504	98.60%	1.40%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	16.70%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1117177660	T -> A	LOC_Os11g29610.1	downstream_gene_variant ; 2470.0bp to feature; MODIFIER	silent_mutation	Average:76.839; most accessible tissue: Callus, score: 89.426	N	N	N	N
vg1117177660	T -> A	LOC_Os11g29620.1	downstream_gene_variant ; 1690.0bp to feature; MODIFIER	silent_mutation	Average:76.839; most accessible tissue: Callus, score: 89.426	N	N	N	N
vg1117177660	T -> A	LOC_Os11g29630.1	downstream_gene_variant ; 2869.0bp to feature; MODIFIER	silent_mutation	Average:76.839; most accessible tissue: Callus, score: 89.426	N	N	N	N
vg1117177660	T -> A	LOC_Os11g29610-LOC_Os11g29620	intergenic_region ; MODIFIER	silent_mutation	Average:76.839; most accessible tissue: Callus, score: 89.426	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1117177660	NA	8.18E-06	mr1188	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
vg1117177660	NA	9.88E-12	mr1232	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
vg1117177660	2.45E-06	2.45E-06	mr1396	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
vg1117177660	NA	1.64E-07	mr1347_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
vg1117177660	NA	5.66E-06	mr1609_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