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Detailed information for vg1110492667:

Variant ID: vg1110492667 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 10492667
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TCATCACCCTCCTGGTAGTAAGTGTAGGGATCCTCCAAAGCTTCATCTCCGACCTCTGATTAAGTTTGTATATTGCAAGGGTGAGTAGCAACCGTACTCA[A/G]
CAAGCCACCACAGCAACAATGCACATGATAGGGGTATTCAAAGGATGGCTATGGTTCTTTTGCGCAAAGCAAGTTTTATAATTCTTTTCACAAACCTAAG

Reverse complement sequence

CTTAGGTTTGTGAAAAGAATTATAAAACTTGCTTTGCGCAAAAGAACCATAGCCATCCTTTGAATACCCCTATCATGTGCATTGTTGCTGTGGTGGCTTG[T/C]
TGAGTACGGTTGCTACTCACCCTTGCAATATACAAACTTAATCAGAGGTCGGAGATGAAGCTTTGGAGGATCCCTACACTTACTACCAGGAGGGTGATGA

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	57.40%	0.10%	4.61%	37.85%	NA
All Indica	2759	39.70%	0.10%	6.42%	53.79%	NA
All Japonica	1512	96.90%	0.10%	0.46%	2.51%	NA
Aus	269	24.90%	0.00%	8.18%	66.91%	NA
Indica I	595	47.40%	0.00%	2.86%	49.75%	NA
Indica II	465	26.00%	0.20%	8.82%	64.95%	NA
Indica III	913	35.60%	0.00%	7.67%	56.74%	NA
Indica Intermediate	786	46.70%	0.30%	6.23%	46.82%	NA
Temperate Japonica	767	99.70%	0.10%	0.00%	0.13%	NA
Tropical Japonica	504	92.70%	0.20%	1.19%	5.95%	NA
Japonica Intermediate	241	96.70%	0.00%	0.41%	2.90%	NA
VI/Aromatic	96	40.60%	0.00%	3.12%	56.25%	NA
Intermediate	90	51.10%	2.20%	10.00%	36.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1110492667	A -> DEL	N	N	silent_mutation	Average:5.752; most accessible tissue: Callus, score: 12.81	N	N	N	N
vg1110492667	A -> G	LOC_Os11g18590.1	upstream_gene_variant ; 637.0bp to feature; MODIFIER	silent_mutation	Average:5.752; most accessible tissue: Callus, score: 12.81	N	N	N	N
vg1110492667	A -> G	LOC_Os11g18580.1	downstream_gene_variant ; 1556.0bp to feature; MODIFIER	silent_mutation	Average:5.752; most accessible tissue: Callus, score: 12.81	N	N	N	N
vg1110492667	A -> G	LOC_Os11g18600.1	downstream_gene_variant ; 1671.0bp to feature; MODIFIER	silent_mutation	Average:5.752; most accessible tissue: Callus, score: 12.81	N	N	N	N
vg1110492667	A -> G	LOC_Os11g18590-LOC_Os11g18600	intergenic_region ; MODIFIER	silent_mutation	Average:5.752; most accessible tissue: Callus, score: 12.81	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1110492667	2.97E-06	2.97E-06	mr1040	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
vg1110492667	NA	2.47E-06	mr1045	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
vg1110492667	NA	4.05E-06	mr1316	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
vg1110492667	NA	4.10E-06	mr1743	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