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Detailed information for vg1113530105:

Variant ID: vg1113530105 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 13530105
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTTACTCATTAATTGCTCAATAAAATTAGCTTTATGCAAATGTTGAACCTAGAGACCCACTATAGGCTAGAAAGCTTGCATACTTCTCTCTCCCTTAT[A/G]
TATATATAATTTTGGGTAAGACTTGCGAGTACAATCTTGTACTTAAACCGGTGTCTGCAATTTCAGGAGAGGATTCCGGTTATGAGTTATGTTTCTTGTG

Reverse complement sequence

CACAAGAAACATAACTCATAACCGGAATCCTCTCCTGAAATTGCAGACACCGGTTTAAGTACAAGATTGTACTCGCAAGTCTTACCCAAAATTATATATA[T/C]
ATAAGGGAGAGAGAAGTATGCAAGCTTTCTAGCCTATAGTGGGTCTCTAGGTTCAACATTTGCATAAAGCTAATTTTATTGAGCAATTAATGAGTAAAAT

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	97.00%	0.30%	0.89%	1.78%	NA
All Indica	2759	95.20%	0.50%	1.38%	2.97%	NA
All Japonica	1512	99.70%	0.10%	0.13%	0.13%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	95.10%	0.50%	0.84%	3.53%	NA
Indica II	465	96.80%	0.60%	1.72%	0.86%	NA
Indica III	913	94.40%	0.40%	0.77%	4.38%	NA
Indica Intermediate	786	95.20%	0.40%	2.29%	2.16%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.20%	0.40%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	98.90%	0.00%	1.11%	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
vg1113530105	A -> DEL	N	N	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23880.1	downstream_gene_variant ; 3848.0bp to feature; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23890.1	downstream_gene_variant ; 2298.0bp to feature; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23880.4	downstream_gene_variant ; 3840.0bp to feature; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23880.2	downstream_gene_variant ; 3848.0bp to feature; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23880.3	downstream_gene_variant ; 3848.0bp to feature; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N
vg1113530105	A -> G	LOC_Os11g23880-LOC_Os11g23890	intergenic_region ; MODIFIER	silent_mutation	Average:22.497; most accessible tissue: Minghui63 young leaf, score: 32.638	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1113530105	4.43E-06	NA	mr1619	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