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Detailed information for vg1112708625:

Variant ID: vg1112708625 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 12708625
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CAGAGTACAAACCAAATTACCTCCAATGAGACATGTAATGGTTGAGGAGGGGCATCGGATCTGAATCGATTCAGATGAGAGCTCTCCTTCCCTTAACCAT[T/A]
CGTTACTCATGATGGTGGTCAACTTCTTCACCGTCTCTTTAAGCATAGCTTTATCGAGAGGATCATTAGAGTTGACCTTGGTCGGTGGTCTCTTCTCGCA

Reverse complement sequence

TGCGAGAAGAGACCACCGACCAAGGTCAACTCTAATGATCCTCTCGATAAAGCTATGCTTAAAGAGACGGTGAAGAAGTTGACCACCATCATGAGTAACG[A/T]
ATGGTTAAGGGAAGGAGAGCTCTCATCTGAATCGATTCAGATCCGATGCCCCTCCTCAACCATTACATGTCTCATTGGAGGTAATTTGGTTTGTACTCTG

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.50%	1.60%	1.40%	3.53%	NA
All Indica	2759	94.90%	2.60%	2.10%	0.36%	NA
All Japonica	1512	98.30%	0.10%	0.00%	1.65%	NA
Aus	269	50.90%	0.00%	2.23%	46.84%	NA
Indica I	595	84.00%	7.70%	8.24%	0.00%	NA
Indica II	465	99.60%	0.00%	0.22%	0.22%	NA
Indica III	913	98.60%	1.00%	0.11%	0.33%	NA
Indica Intermediate	786	96.20%	2.20%	0.89%	0.76%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	95.00%	0.00%	0.00%	4.96%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	0.00%	0.00%	4.17%	NA
Intermediate	90	93.30%	2.20%	2.22%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1112708625	T -> A	LOC_Os11g22154.1	missense_variant ; p.Glu181Val; MODERATE	nonsynonymous_codon ; E181V	Average:44.611; most accessible tissue: Minghui63 flag leaf, score: 65.44	unknown	unknown	DELETERIOUS	0.01
vg1112708625	T -> DEL	LOC_Os11g22154.1	N	frameshift_variant	Average:44.611; most accessible tissue: Minghui63 flag leaf, score: 65.44	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1112708625	2.30E-07	2.15E-09	mr1097_2	Ind_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
vg1112708625	6.23E-08	1.39E-08	mr1154_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
vg1112708625	NA	2.53E-06	mr1223_2	Ind_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