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Detailed information for vg1105334970:

Variant ID: vg1105334970 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5334970
Reference Allele: T	Alternative Allele: G
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.80, G: 0.19, others allele: 0.00, population size: 108. )

Flanking Sequence (100 bp) in Reference Genome:

ATATAGTATTATTTTTAACACAAAACAAACATATAATAAAAATATATTCAATGTTAGATTTAATAAAACTAATTTGATATTTCAGATGTTGCTAAAATTT[T/G]
TTTATAAACTTGGTCAAACTCAATAAAGTTTGATTAGAAAAAAGTCAAATGACTTATAACATGAAACAGAAGGAATAATTATTTTTGACATGTATCATGG

Reverse complement sequence

CCATGATACATGTCAAAAATAATTATTCCTTCTGTTTCATGTTATAAGTCATTTGACTTTTTTCTAATCAAACTTTATTGAGTTTGACCAAGTTTATAAA[A/C]
AAATTTTAGCAACATCTGAAATATCAAATTAGTTTTATTAAATCTAACATTGAATATATTTTTATTATATGTTTGTTTTGTGTTAAAAATAATACTATAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	54.40%	40.40%	0.51%	4.68%	NA
All Indica	2759	80.20%	14.60%	0.36%	4.82%	NA
All Japonica	1512	9.30%	90.70%	0.00%	0.00%	NA
Aus	269	58.40%	9.30%	0.74%	31.60%	NA
Indica I	595	78.00%	4.90%	1.01%	16.13%	NA
Indica II	465	91.40%	8.40%	0.22%	0.00%	NA
Indica III	913	84.40%	14.70%	0.11%	0.77%	NA
Indica Intermediate	786	70.50%	25.40%	0.25%	3.82%	NA
Temperate Japonica	767	3.00%	97.00%	0.00%	0.00%	NA
Tropical Japonica	504	20.00%	80.00%	0.00%	0.00%	NA
Japonica Intermediate	241	7.10%	92.90%	0.00%	0.00%	NA
VI/Aromatic	96	7.30%	81.20%	11.46%	0.00%	NA
Intermediate	90	56.70%	38.90%	1.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105334970	T -> DEL	N	N	silent_mutation	Average:24.013; most accessible tissue: Callus, score: 50.153	N	N	N	N
vg1105334970	T -> G	LOC_Os11g09950.1	downstream_gene_variant ; 1858.0bp to feature; MODIFIER	silent_mutation	Average:24.013; most accessible tissue: Callus, score: 50.153	N	N	N	N
vg1105334970	T -> G	LOC_Os11g09960.1	downstream_gene_variant ; 1554.0bp to feature; MODIFIER	silent_mutation	Average:24.013; most accessible tissue: Callus, score: 50.153	N	N	N	N
vg1105334970	T -> G	LOC_Os11g09950-LOC_Os11g09960	intergenic_region ; MODIFIER	silent_mutation	Average:24.013; most accessible tissue: Callus, score: 50.153	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105334970	NA	2.38E-09	mr1352	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
vg1105334970	1.62E-06	1.62E-06	mr1770	Jap_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
vg1105334970	NA	7.93E-06	mr1460_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
vg1105334970	NA	6.22E-07	mr1517_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
vg1105334970	NA	2.07E-06	mr1538_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
vg1105334970	NA	2.31E-06	mr1594_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
vg1105334970	NA	1.28E-06	mr1624_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
vg1105334970	NA	3.57E-08	mr1758_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