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Detailed information for vg1127723741:

Variant ID: vg1127723741 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 27723741
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 50. )

Flanking Sequence (100 bp) in Reference Genome:

GTGTGTTTATTTCACGTCAAAATTGAAAGTTTGGTTGAAATTGGAACGATGCGACGGAAAAGTTCGAAATTTAACACCATATGTGTACAAAAATTTTGAT[G/A]
TGATAGAAAAATTAAAAGTTCGAAGAAAAAGTTTGTAACTAAACTTGGCCTAGGTTGTTTTTTTTGGATGGCGTAGGTTGTTTTTTTTTTTTTTATGGAG

Reverse complement sequence

CTCCATAAAAAAAAAAAAAACAACCTACGCCATCCAAAAAAAACAACCTAGGCCAAGTTTAGTTACAAACTTTTTCTTCGAACTTTTAATTTTTCTATCA[C/T]
ATCAAAATTTTTGTACACATATGGTGTTAAATTTCGAACTTTTCCGTCGCATCGTTCCAATTTCAACCAAACTTTCAATTTTGACGTGAAATAAACACAC

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	53.70%	17.60%	0.53%	28.18%	NA
All Indica	2759	48.90%	23.50%	0.47%	27.15%	NA
All Japonica	1512	68.30%	10.50%	0.46%	20.70%	NA
Aus	269	27.90%	0.70%	1.12%	70.26%	NA
Indica I	595	54.80%	5.20%	1.18%	38.82%	NA
Indica II	465	60.90%	6.90%	0.22%	32.04%	NA
Indica III	913	38.30%	48.30%	0.11%	13.25%	NA
Indica Intermediate	786	49.50%	18.40%	0.51%	31.55%	NA
Temperate Japonica	767	74.70%	7.30%	0.26%	17.73%	NA
Tropical Japonica	504	52.40%	18.30%	0.99%	28.37%	NA
Japonica Intermediate	241	81.30%	4.60%	0.00%	14.11%	NA
VI/Aromatic	96	30.20%	2.10%	2.08%	65.62%	NA
Intermediate	90	60.00%	20.00%	0.00%	20.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1127723741	G -> A	LOC_Os11g45820.1	upstream_gene_variant ; 95.0bp to feature; MODIFIER	silent_mutation	Average:38.197; most accessible tissue: Callus, score: 92.943	N	N	N	N
vg1127723741	G -> A	LOC_Os11g45809.1	downstream_gene_variant ; 2641.0bp to feature; MODIFIER	silent_mutation	Average:38.197; most accessible tissue: Callus, score: 92.943	N	N	N	N
vg1127723741	G -> A	LOC_Os11g45809-LOC_Os11g45820	intergenic_region ; MODIFIER	silent_mutation	Average:38.197; most accessible tissue: Callus, score: 92.943	N	N	N	N
vg1127723741	G -> DEL	N	N	silent_mutation	Average:38.197; most accessible tissue: Callus, score: 92.943	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1127723741	NA	6.26E-06	mr1044	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
vg1127723741	2.71E-06	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
vg1127723741	NA	1.39E-08	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
vg1127723741	3.36E-06	6.53E-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
vg1127723741	4.81E-08	NA	mr1133_2	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
vg1127723741	NA	1.06E-08	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
vg1127723741	3.98E-06	NA	mr1667_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
vg1127723741	NA	8.10E-07	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