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Detailed information for vg1112908740:

Variant ID: vg1112908740 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12908740
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AAACGACAAACAAAGCACACAAGAAATACCAGCAATGAGGCTACTGAAACAGCAAAAGAAACCAATTTTAATGGATTCTATACATTTTAACGGATTCACT[A/G]
CAATTTGAATGGGTTAAAATGGAGCTCAGATTATTTAGTTACGAATTTTATAATATGAGTTGCGTTATTACTAATAACTGAAAAACCTTAATCATTTATT

Reverse complement sequence

AATAAATGATTAAGGTTTTTCAGTTATTAGTAATAACGCAACTCATATTATAAAATTCGTAACTAAATAATCTGAGCTCCATTTTAACCCATTCAAATTG[T/C]
AGTGAATCCGTTAAAATGTATAGAATCCATTAAAATTGGTTTCTTTTGCTGTTTCAGTAGCCTCATTGCTGGTATTTCTTGTGTGCTTTGTTTGTCGTTT

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	75.40%	0.10%	3.20%	21.29%	NA
All Indica	2759	59.80%	0.10%	5.26%	34.76%	NA
All Japonica	1512	97.40%	0.00%	0.40%	2.25%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	63.70%	0.30%	2.18%	33.78%	NA
Indica II	465	76.30%	0.20%	2.15%	21.29%	NA
Indica III	913	45.00%	0.00%	9.97%	45.02%	NA
Indica Intermediate	786	64.40%	0.10%	3.94%	31.55%	NA
Temperate Japonica	767	99.20%	0.00%	0.26%	0.52%	NA
Tropical Japonica	504	93.80%	0.00%	0.79%	5.36%	NA
Japonica Intermediate	241	98.80%	0.00%	0.00%	1.24%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	85.60%	0.00%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112908740	A -> DEL	N	N	silent_mutation	Average:27.503; most accessible tissue: Callus, score: 66.439	N	N	N	N
vg1112908740	A -> G	LOC_Os11g22460.1	upstream_gene_variant ; 1264.0bp to feature; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Callus, score: 66.439	N	N	N	N
vg1112908740	A -> G	LOC_Os11g22449.1	downstream_gene_variant ; 3247.0bp to feature; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Callus, score: 66.439	N	N	N	N
vg1112908740	A -> G	LOC_Os11g22460-LOC_Os11g22470	intergenic_region ; MODIFIER	silent_mutation	Average:27.503; most accessible tissue: Callus, score: 66.439	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112908740	2.21E-06	1.33E-07	mr1167_2	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