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Detailed information for vg1106469220:

Variant ID: vg1106469220 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6469220
Reference Allele: A	Alternative Allele: G,T
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 268. )

Flanking Sequence (100 bp) in Reference Genome:

ACATATTAGCTTAAATCGAAACACCTTAACTTTGGATGCACTAATTTTTAGTGGACCTGTTTAGTCTCACAACTCGTATGTGTTAGTATTAATCTTGACT[A/G,T]
GTAGGCTTGATATATCCTTAATTGCATGTGTTGTGTATAGGCAGCAACGTGAAGTACGTGTTTGTGTTTGCATGGTAGACTAACTAATTTGTTAGTGCAT

Reverse complement sequence

ATGCACTAACAAATTAGTTAGTCTACCATGCAAACACAAACACGTACTTCACGTTGCTGCCTATACACAACACATGCAATTAAGGATATATCAAGCCTAC[T/C,A]
AGTCAAGATTAATACTAACACATACGAGTTGTGAGACTAAACAGGTCCACTAAAAATTAGTGCATCCAAAGTTAAGGTGTTTCGATTTAAGCTAATATGT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	95.00%	3.70%	0.23%	1.04%	T: 0.02%
All Indica	2759	97.80%	0.30%	0.14%	1.78%	NA
All Japonica	1512	88.60%	11.00%	0.46%	0.00%	NA
Aus	269	99.60%	0.00%	0.00%	0.00%	T: 0.37%
Indica I	595	97.80%	0.00%	0.17%	2.02%	NA
Indica II	465	98.90%	0.00%	0.00%	1.08%	NA
Indica III	913	97.70%	0.10%	0.00%	2.19%	NA
Indica Intermediate	786	97.30%	0.80%	0.38%	1.53%	NA
Temperate Japonica	767	98.80%	0.90%	0.26%	0.00%	NA
Tropical Japonica	504	70.80%	28.80%	0.40%	0.00%	NA
Japonica Intermediate	241	92.90%	5.80%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg1106469220	A -> T	LOC_Os11g11640.1	upstream_gene_variant ; 4112.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> T	LOC_Os11g11620.1	downstream_gene_variant ; 3940.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> T	LOC_Os11g11630.1	downstream_gene_variant ; 2325.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> T	LOC_Os11g11620-LOC_Os11g11630	intergenic_region ; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> DEL	N	N	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> G	LOC_Os11g11640.1	upstream_gene_variant ; 4112.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> G	LOC_Os11g11620.1	downstream_gene_variant ; 3940.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> G	LOC_Os11g11630.1	downstream_gene_variant ; 2325.0bp to feature; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N
vg1106469220	A -> G	LOC_Os11g11620-LOC_Os11g11630	intergenic_region ; MODIFIER	silent_mutation	Average:59.665; most accessible tissue: Callus, score: 70.366	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106469220	2.25E-06	NA	mr1836	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