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Detailed information for vg1127480962:

Variant ID: vg1127480962 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27480962
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CTCTTACACAACAATCTTGCTCTACTAGCTAGTGTATTATATATAGAACATGTTGGTGAGAGAATTTTATGTTTGCTATCAGTATGTAATACTCTTGGGA[G/T]
ATTCGAGGAAAACAAAATATGCATCTCGTACTCTAAACCTCACTATTGCATTGTTCTCCACTTATATTATTCATGTAGTAACATCTGATATGTTATTTAC

Reverse complement sequence

GTAAATAACATATCAGATGTTACTACATGAATAATATAAGTGGAGAACAATGCAATAGTGAGGTTTAGAGTACGAGATGCATATTTTGTTTTCCTCGAAT[C/A]
TCCCAAGAGTATTACATACTGATAGCAAACATAAAATTCTCTCACCAACATGTTCTATATATAATACACTAGCTAGTAGAGCAAGATTGTTGTGTAAGAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.20%	2.70%	0.15%	0.00%	NA
All Indica	2759	99.30%	0.60%	0.07%	0.00%	NA
All Japonica	1512	92.80%	6.90%	0.26%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	97.10%	2.70%	0.17%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	99.90%	0.00%	0.11%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	88.90%	10.70%	0.39%	0.00%	NA
Tropical Japonica	504	99.20%	0.60%	0.20%	0.00%	NA
Japonica Intermediate	241	91.70%	8.30%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	94.40%	4.40%	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
vg1127480962	G -> T	LOC_Os11g45390-LOC_Os11g45400	intergenic_region ; MODIFIER	silent_mutation	Average:50.464; most accessible tissue: Callus, score: 79.389	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127480962	8.39E-08	8.39E-08	mr1191_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