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Detailed information for vg1125312631:

Variant ID: vg1125312631 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 25312631
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.95, A: 0.05, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

ATTGAGAGAAGAGTCAATATAAAAACCCGATACGAGATTAATCAAAATTTAGAATAAAAATAAAATAAAATCCAAAATTAGAAAAGAAAAGGAGAGTCCA[T/A]
GTAGGAATACAATTTAAAAATAACTGAAATTCGGAATTAAAAATCAGGAATATTAAGAGAAGAGTCGATATAAGAACCTAATACGAGATTAATTAATATT

Reverse complement sequence

AATATTAATTAATCTCGTATTAGGTTCTTATATCGACTCTTCTCTTAATATTCCTGATTTTTAATTCCGAATTTCAGTTATTTTTAAATTGTATTCCTAC[A/T]
TGGACTCTCCTTTTCTTTTCTAATTTTGGATTTTATTTTATTTTTATTCTAAATTTTGATTAATCTCGTATCGGGTTTTTATATTGACTCTTCTCTCAAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	42.00%	22.20%	0.28%	35.46%	NA
All Indica	2759	61.10%	13.40%	0.04%	25.48%	NA
All Japonica	1512	14.60%	36.20%	0.66%	48.61%	NA
Aus	269	17.80%	22.30%	0.37%	59.48%	NA
Indica I	595	42.70%	6.10%	0.17%	51.09%	NA
Indica II	465	27.30%	38.90%	0.00%	33.76%	NA
Indica III	913	86.60%	4.20%	0.00%	9.20%	NA
Indica Intermediate	786	65.30%	14.60%	0.00%	20.10%	NA
Temperate Japonica	767	3.10%	55.30%	0.78%	40.81%	NA
Tropical Japonica	504	31.30%	10.70%	0.20%	57.74%	NA
Japonica Intermediate	241	15.80%	28.60%	1.24%	54.36%	NA
VI/Aromatic	96	1.00%	54.20%	0.00%	44.79%	NA
Intermediate	90	35.60%	24.40%	1.11%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1125312631	T -> A	LOC_Os11g42060.1	downstream_gene_variant ; 3238.0bp to feature; MODIFIER	silent_mutation	Average:22.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1125312631	T -> A	LOC_Os11g42050-LOC_Os11g42060	intergenic_region ; MODIFIER	silent_mutation	Average:22.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N
vg1125312631	T -> DEL	N	N	silent_mutation	Average:22.675; most accessible tissue: Minghui63 panicle, score: 50.413	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1125312631	9.41E-07	1.08E-17	mr1133	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
vg1125312631	NA	3.59E-11	mr1133	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
vg1125312631	NA	2.15E-07	mr1667	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
vg1125312631	NA	9.85E-07	mr1133_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