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Detailed information for vg1109243978:

Variant ID: vg1109243978 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 9243978
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AACAACACAACCTGGTAGACCTGGTTATCAATTCAATTTCTGGGTGTAACAAAAACGATGACGGGAGATGGATCATCCCCTTACTTTATAACGATTACAA[A/G]
TGCACAAACCATGCGTACATTCAACATGTACCCCATACATATACTACCTCCTTTTTTTTAAGTATATGTCGCCGTTAATTTTGATAAATATTTGACCATT

Reverse complement sequence

AATGGTCAAATATTTATCAAAATTAACGGCGACATATACTTAAAAAAAAGGAGGTAGTATATGTATGGGGTACATGTTGAATGTACGCATGGTTTGTGCA[T/C]
TTGTAATCGTTATAAAGTAAGGGGATGATCCATCTCCCGTCATCGTTTTTGTTACACCCAGAAATTGAATTGATAACCAGGTCTACCAGGTTGTGTTGTT

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	89.50%	0.40%	1.44%	8.68%	NA
All Indica	2759	82.80%	0.60%	2.36%	14.24%	NA
All Japonica	1512	98.90%	0.00%	0.20%	0.93%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	82.00%	1.80%	4.37%	11.76%	NA
Indica II	465	90.50%	0.00%	0.65%	8.82%	NA
Indica III	913	84.30%	0.10%	0.66%	14.90%	NA
Indica Intermediate	786	77.10%	0.50%	3.82%	18.58%	NA
Temperate Japonica	767	98.00%	0.00%	0.39%	1.56%	NA
Tropical Japonica	504	99.80%	0.00%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	99.00%	0.00%	0.00%	1.04%	NA
Intermediate	90	96.70%	1.10%	0.00%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1109243978	A -> DEL	N	N	silent_mutation	Average:30.563; most accessible tissue: Callus, score: 58.271	N	N	N	N
vg1109243978	A -> G	LOC_Os11g16670.1	upstream_gene_variant ; 1083.0bp to feature; MODIFIER	silent_mutation	Average:30.563; most accessible tissue: Callus, score: 58.271	N	N	N	N
vg1109243978	A -> G	LOC_Os11g16680.1	downstream_gene_variant ; 423.0bp to feature; MODIFIER	silent_mutation	Average:30.563; most accessible tissue: Callus, score: 58.271	N	N	N	N
vg1109243978	A -> G	LOC_Os11g16670-LOC_Os11g16680	intergenic_region ; MODIFIER	silent_mutation	Average:30.563; most accessible tissue: Callus, score: 58.271	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1109243978	2.54E-06	1.97E-06	mr1043_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
vg1109243978	NA	6.32E-06	mr1291_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
vg1109243978	NA	5.49E-06	mr1479_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