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Detailed information for vg1104766707:

Variant ID: vg1104766707 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 4766707
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: 291. )

Flanking Sequence (100 bp) in Reference Genome:

CTGCAAGAGGTAAATGGCAATATGTGCGGGCAGAGGTAGAGTCCATGTTTCATTTGGGTCGTCCAGTTTTAGTTGGCACTACAAGGTGAACTTCCTTATA[G/T]
CAAATCCATTTTGTTGCAATCCAAAACAATATGTTCACGACTGCTTGAAATAACATCAAATGTACTTTATGAACTATGACTATTAGATTCCATCACCTGA

Reverse complement sequence

TCAGGTGATGGAATCTAATAGTCATAGTTCATAAAGTACATTTGATGTTATTTCAAGCAGTCGTGAACATATTGTTTTGGATTGCAACAAAATGGATTTG[C/A]
TATAAGGAAGTTCACCTTGTAGTGCCAACTAAAACTGGACGACCCAAATGAAACATGGACTCTACCTCTGCCCGCACATATTGCCATTTACCTCTTGCAG

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	92.40%	7.40%	0.15%	0.00%	NA
All Indica	2759	92.70%	7.30%	0.04%	0.00%	NA
All Japonica	1512	90.70%	8.90%	0.40%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	96.60%	3.40%	0.00%	0.00%	NA
Indica II	465	97.20%	2.80%	0.00%	0.00%	NA
Indica III	913	93.50%	6.50%	0.00%	0.00%	NA
Indica Intermediate	786	86.00%	13.90%	0.13%	0.00%	NA
Temperate Japonica	767	93.00%	6.30%	0.78%	0.00%	NA
Tropical Japonica	504	93.80%	6.20%	0.00%	0.00%	NA
Japonica Intermediate	241	76.80%	23.20%	0.00%	0.00%	NA
VI/Aromatic	96	89.60%	10.40%	0.00%	0.00%	NA
Intermediate	90	94.40%	5.60%	0.00%	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
vg1104766707	G -> T	LOC_Os11g08980.1	intron_variant ; MODIFIER	silent_mutation	Average:46.252; most accessible tissue: Callus, score: 68.41	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1104766707	3.04E-06	NA	mr1719	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