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Detailed information for vg1105101275:

Variant ID: vg1105101275 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5101275
Reference Allele: T	Alternative Allele: G
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATTCGGAAAAAAATAGTAATATTTTTAACCCAAAACAAATTTATTATGAAAATATATTCAATTATTGATTTGATGAAACTAATTTAGTATTATAAATAT[T/G]
ACTATATTTGTCTATAAACTTAGTCAAACTTAAAACACGTCTTATAACATGAAACGGAGGGTGTACTTATTACTACTATATATGCTGATGGTCATAATGG

Reverse complement sequence

CCATTATGACCATCAGCATATATAGTAGTAATAAGTACACCCTCCGTTTCATGTTATAAGACGTGTTTTAAGTTTGACTAAGTTTATAGACAAATATAGT[A/C]
ATATTTATAATACTAAATTAGTTTCATCAAATCAATAATTGAATATATTTTCATAATAAATTTGTTTTGGGTTAAAAATATTACTATTTTTTTCCGAATT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	78.00%	18.30%	2.96%	0.68%	NA
All Indica	2759	92.10%	7.10%	0.62%	0.18%	NA
All Japonica	1512	47.00%	43.30%	7.94%	1.79%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	97.10%	2.50%	0.34%	0.00%	NA
Indica II	465	96.80%	2.60%	0.22%	0.43%	NA
Indica III	913	93.20%	6.60%	0.22%	0.00%	NA
Indica Intermediate	786	84.10%	14.00%	1.53%	0.38%	NA
Temperate Japonica	767	47.20%	41.90%	8.21%	2.74%	NA
Tropical Japonica	504	35.70%	54.00%	9.33%	0.99%	NA
Japonica Intermediate	241	69.70%	25.70%	4.15%	0.41%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	83.30%	13.30%	3.33%	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
vg1105101275	T -> DEL	N	N	silent_mutation	Average:18.392; most accessible tissue: Callus, score: 43.707	N	N	N	N
vg1105101275	T -> G	LOC_Os11g09510.1	upstream_gene_variant ; 1455.0bp to feature; MODIFIER	silent_mutation	Average:18.392; most accessible tissue: Callus, score: 43.707	N	N	N	N
vg1105101275	T -> G	LOC_Os11g09520.1	downstream_gene_variant ; 2503.0bp to feature; MODIFIER	silent_mutation	Average:18.392; most accessible tissue: Callus, score: 43.707	N	N	N	N
vg1105101275	T -> G	LOC_Os11g09510-LOC_Os11g09520	intergenic_region ; MODIFIER	silent_mutation	Average:18.392; most accessible tissue: Callus, score: 43.707	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105101275	NA	1.97E-06	mr1662_2	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
vg1105101275	2.99E-06	NA	mr1713_2	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