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Detailed information for vg1106330395:

Variant ID: vg1106330395 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6330395
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

CTTCACAAGTAAGGTGGACATGTCCAGATAAAATCCAATTCAGCTTCTTGAGAAACGTTGTCTTCGAATTTGCATATCTCTTCTCTCTTCGTATTTTAAT[G/A]
TATGACGCCGTTGTCTTTTTAACAAACGTTTGACCTTTCGTCTTATTCAAAAAATTTATGTAATTATCATTTATTTTATTGTGACTTGATTTATCATCAA

Reverse complement sequence

TTGATGATAAATCAAGTCACAATAAAATAAATGATAATTACATAAATTTTTTGAATAAGACGAAAGGTCAAACGTTTGTTAAAAAGACAACGGCGTCATA[C/T]
ATTAAAATACGAAGAGAGAAGAGATATGCAAATTCGAAGACAACGTTTCTCAAGAAGCTGAATTGGATTTTATCTGGACATGTCCACCTTACTTGTGAAG

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	90.80%	8.80%	0.40%	0.00%	NA
All Indica	2759	99.10%	0.90%	0.04%	0.00%	NA
All Japonica	1512	74.10%	24.80%	1.12%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	97.60%	2.40%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.10%	0.13%	0.00%	NA
Temperate Japonica	767	78.50%	19.90%	1.56%	0.00%	NA
Tropical Japonica	504	79.80%	19.80%	0.40%	0.00%	NA
Japonica Intermediate	241	48.10%	50.60%	1.24%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	3.30%	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
vg1106330395	G -> A	LOC_Os11g11400.1	downstream_gene_variant ; 1320.0bp to feature; MODIFIER	silent_mutation	Average:35.877; most accessible tissue: Callus, score: 50.138	N	N	N	N
vg1106330395	G -> A	LOC_Os11g11390-LOC_Os11g11400	intergenic_region ; MODIFIER	silent_mutation	Average:35.877; most accessible tissue: Callus, score: 50.138	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106330395	1.89E-06	NA	mr1672	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