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Detailed information for vg1106186411:

Variant ID: vg1106186411 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 6186411
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: 126. )

Flanking Sequence (100 bp) in Reference Genome:

GCAGGCTAGAGATTGATATTCTAAGCACGACTTAATAGATCAGACTCAACTGATGCAGCATTAAGTATGAAAAGAAGAACAATATCTAGACAATCAAGCC[G/A]
CTGGAAGTTTCATAGAGTGGTAGATATCTTATATAATCTAAACCAATGTCGATATTTAACCTAACTGGTTGCCCTCTTTTAACAGATGTTAGCCGATTGT

Reverse complement sequence

ACAATCGGCTAACATCTGTTAAAAGAGGGCAACCAGTTAGGTTAAATATCGACATTGGTTTAGATTATATAAGATATCTACCACTCTATGAAACTTCCAG[C/T]
GGCTTGATTGTCTAGATATTGTTCTTCTTTTCATACTTAATGCTGCATCAGTTGAGTCTGATCTATTAAGTCGTGCTTAGAATATCAATCTCTAGCCTGC

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	85.40%	14.60%	0.08%	0.00%	NA
All Indica	2759	76.70%	23.20%	0.11%	0.00%	NA
All Japonica	1512	99.30%	0.70%	0.07%	0.00%	NA
Aus	269	93.70%	6.30%	0.00%	0.00%	NA
Indica I	595	70.30%	29.70%	0.00%	0.00%	NA
Indica II	465	81.30%	18.30%	0.43%	0.00%	NA
Indica III	913	78.20%	21.70%	0.11%	0.00%	NA
Indica Intermediate	786	77.00%	23.00%	0.00%	0.00%	NA
Temperate Japonica	767	99.60%	0.40%	0.00%	0.00%	NA
Tropical Japonica	504	99.20%	0.80%	0.00%	0.00%	NA
Japonica Intermediate	241	98.30%	1.20%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	77.80%	22.20%	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
vg1106186411	G -> A	LOC_Os11g11170.1	upstream_gene_variant ; 2980.0bp to feature; MODIFIER	silent_mutation	Average:29.051; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1106186411	G -> A	LOC_Os11g11180.1	downstream_gene_variant ; 3779.0bp to feature; MODIFIER	silent_mutation	Average:29.051; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N
vg1106186411	G -> A	LOC_Os11g11170-LOC_Os11g11180	intergenic_region ; MODIFIER	silent_mutation	Average:29.051; most accessible tissue: Minghui63 panicle, score: 53.77	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1106186411	2.77E-06	2.77E-06	mr1456_2	Ind_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
vg1106186411	8.82E-06	9.97E-06	mr1577_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