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Detailed information for vg1126079756:

Variant ID: vg1126079756 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 26079756
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.77, A: 0.23, others allele: 0.00, population size: 74. )

Flanking Sequence (100 bp) in Reference Genome:

CTGATATTCTCTCCCCCAATCAGTCTGCATGGCAAAGATTTTTCTATCAAACATTCGTTCTACTAGTGCTTGGAATTGTTTAAACTTCTCAAAAACTTCA[G/A]
ACTTATATTTTAGCAGGTATATCCAGGTAAACTTACTAAAATCATCAATAAAACTCACATAATATTTGTTTCTCCTAACTCTGGGGCAGGACCCCAAACA

Reverse complement sequence

TGTTTGGGGTCCTGCCCCAGAGTTAGGAGAAACAAATATTATGTGAGTTTTATTGATGATTTTAGTAAGTTTACCTGGATATACCTGCTAAAATATAAGT[C/T]
TGAAGTTTTTGAGAAGTTTAAACAATTCCAAGCACTAGTAGAACGAATGTTTGATAGAAAAATCTTTGCCATGCAGACTGATTGGGGGAGAGAATATCAG

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	75.90%	6.50%	0.76%	16.86%	NA
All Indica	2759	69.30%	6.10%	1.09%	23.49%	NA
All Japonica	1512	85.90%	8.30%	0.26%	5.56%	NA
Aus	269	98.90%	0.40%	0.00%	0.74%	NA
Indica I	595	79.20%	1.70%	0.84%	18.32%	NA
Indica II	465	55.30%	5.80%	1.94%	36.99%	NA
Indica III	913	69.90%	7.40%	0.44%	22.23%	NA
Indica Intermediate	786	69.60%	8.00%	1.53%	20.87%	NA
Temperate Japonica	767	89.70%	9.10%	0.00%	1.17%	NA
Tropical Japonica	504	81.90%	7.90%	0.40%	9.72%	NA
Japonica Intermediate	241	82.20%	6.20%	0.83%	10.79%	NA
VI/Aromatic	96	42.70%	3.10%	2.08%	52.08%	NA
Intermediate	90	76.70%	8.90%	0.00%	14.44%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1126079756	G -> A	LOC_Os11g43240.1	upstream_gene_variant ; 2130.0bp to feature; MODIFIER	silent_mutation	Average:22.435; most accessible tissue: Callus, score: 44.243	N	N	N	N
vg1126079756	G -> A	LOC_Os11g43230.1	intron_variant ; MODIFIER	silent_mutation	Average:22.435; most accessible tissue: Callus, score: 44.243	N	N	N	N
vg1126079756	G -> DEL	N	N	silent_mutation	Average:22.435; most accessible tissue: Callus, score: 44.243	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1126079756	2.18E-07	NA	mr1122	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
vg1126079756	NA	6.19E-06	mr1280	Jap_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
vg1126079756	4.43E-09	4.43E-09	mr1191_2	Jap_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