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Detailed information for vg1118275729:

Variant ID: vg1118275729 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 18275729
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 331. )

Flanking Sequence (100 bp) in Reference Genome:

GCTACAAGATTGTCCAACGTTCAATCTGTAACATTTCTTCTAATATGCATAACTTGATAGCTTTGCTTGCCTTCCTTTAAATCCATATAAGTGAAATTGA[C/T]
CTATTTAACTGAAATGTCTTTGATATTATGTCCATACATATATACTTTATAGCTTTGCTTGCTTGCCATGTGCATCCATGTGTGCATAAACCGCTGCTCT

Reverse complement sequence

AGAGCAGCGGTTTATGCACACATGGATGCACATGGCAAGCAAGCAAAGCTATAAAGTATATATGTATGGACATAATATCAAAGACATTTCAGTTAAATAG[G/A]
TCAATTTCACTTATATGGATTTAAAGGAAGGCAAGCAAAGCTATCAAGTTATGCATATTAGAAGAAATGTTACAGATTGAACGTTGGACAATCTTGTAGC

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	96.30%	2.10%	1.54%	0.00%	NA
All Indica	2759	97.80%	1.90%	0.29%	0.00%	NA
All Japonica	1512	92.70%	3.10%	4.23%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.80%	0.70%	0.50%	0.00%	NA
Indica II	465	95.30%	4.70%	0.00%	0.00%	NA
Indica III	913	99.00%	1.00%	0.00%	0.00%	NA
Indica Intermediate	786	97.10%	2.30%	0.64%	0.00%	NA
Temperate Japonica	767	85.90%	6.10%	7.95%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	97.80%	1.10%	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
vg1118275729	C -> T	LOC_Os11g31320-LOC_Os11g31330	intergenic_region ; MODIFIER	silent_mutation	Average:33.791; most accessible tissue: Callus, score: 60.384	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1118275729	2.51E-06	NA	mr1295_2	Jap_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
vg1118275729	NA	6.48E-06	mr1398_2	Jap_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