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Detailed information for vg1127764793:

Variant ID: vg1127764793 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27764793
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.91, A: 0.09, others allele: 0.00, population size: 81. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGATCTGAGCTTCTAATTCCTCCCATTGGAAAAATATGATAAGCTGCAGTGCATAGAGGGGTAAAACTTAGCATTTTGTACAATGGTTTGTACCAAAA[A/T]
TTTATAAAAACATACCACTTGGATCTAACAAAACGGTCAAAGATCATAGAATTTGGTAAAGGGAGAGCAATAATCTGTACTAGAATGCCAGAAGTCTCCC

Reverse complement sequence

GGGAGACTTCTGGCATTCTAGTACAGATTATTGCTCTCCCTTTACCAAATTCTATGATCTTTGACCGTTTTGTTAGATCCAAGTGGTATGTTTTTATAAA[T/A]
TTTTGGTACAAACCATTGTACAAAATGCTAAGTTTTACCCCTCTATGCACTGCAGCTTATCATATTTTTCCAATGGGAGGAATTAGAAGCTCAGATCAAA

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	38.60%	25.20%	0.44%	35.72%	NA
All Indica	2759	26.60%	32.70%	0.36%	40.41%	NA
All Japonica	1512	64.70%	14.00%	0.40%	20.90%	NA
Aus	269	18.60%	14.50%	0.37%	66.54%	NA
Indica I	595	25.40%	18.80%	0.50%	55.29%	NA
Indica II	465	26.50%	11.20%	0.86%	61.51%	NA
Indica III	913	29.10%	53.70%	0.00%	17.20%	NA
Indica Intermediate	786	24.60%	31.40%	0.38%	43.64%	NA
Temperate Japonica	767	68.60%	14.30%	0.52%	16.56%	NA
Tropical Japonica	504	52.60%	17.50%	0.40%	29.56%	NA
Japonica Intermediate	241	78.00%	5.40%	0.00%	16.60%	NA
VI/Aromatic	96	29.20%	9.40%	2.08%	59.38%	NA
Intermediate	90	37.80%	36.70%	2.22%	23.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127764793	A -> T	LOC_Os11g45890.1	upstream_gene_variant ; 3146.0bp to feature; MODIFIER	silent_mutation	Average:44.432; most accessible tissue: Callus, score: 80.347	N	N	N	N
vg1127764793	A -> T	LOC_Os11g45899.1	upstream_gene_variant ; 138.0bp to feature; MODIFIER	silent_mutation	Average:44.432; most accessible tissue: Callus, score: 80.347	N	N	N	N
vg1127764793	A -> T	LOC_Os11g45908.1	upstream_gene_variant ; 3210.0bp to feature; MODIFIER	silent_mutation	Average:44.432; most accessible tissue: Callus, score: 80.347	N	N	N	N
vg1127764793	A -> T	LOC_Os11g45890-LOC_Os11g45899	intergenic_region ; MODIFIER	silent_mutation	Average:44.432; most accessible tissue: Callus, score: 80.347	N	N	N	N
vg1127764793	A -> DEL	N	N	silent_mutation	Average:44.432; most accessible tissue: Callus, score: 80.347	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127764793	2.49E-08	NA	mr1133	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
vg1127764793	9.52E-07	6.52E-12	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
vg1127764793	NA	1.62E-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
vg1127764793	4.79E-07	1.11E-11	mr1133_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
vg1127764793	NA	2.22E-08	mr1667_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