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Detailed information for vg1105257664:

Variant ID: vg1105257664 (JBrowse)	Variation Type: SNP
Chromosome: chr11	Position: 5257664
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 73. )

Flanking Sequence (100 bp) in Reference Genome:

GCTAAATAAATCGACAACCCAAAACTCCCTTATCCTATCTCGATATTGTCACTCTCTCAAACTCTCGCCCGGCGATTACTTAAAACCCCTCTATCAACTC[A/G]
AACCCGATGAACCCCCTCGAATATGTATAATCGATCGGTGTATTTATTTACCGTGCGTCGATTCGAATATCTCGATTTTATTACTACCACAACGATTGGA

Reverse complement sequence

TCCAATCGTTGTGGTAGTAATAAAATCGAGATATTCGAATCGACGCACGGTAAATAAATACACCGATCGATTATACATATTCGAGGGGGTTCATCGGGTT[T/C]
GAGTTGATAGAGGGGTTTTAAGTAATCGCCGGGCGAGAGTTTGAGAGAGTGACAATATCGAGATAGGATAAGGGAGTTTTGGGTTGTCGATTTATTTAGC

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	24.50%	3.70%	0.08%	71.73%	NA
All Indica	2759	8.90%	1.20%	0.11%	89.78%	NA
All Japonica	1512	58.70%	9.10%	0.00%	32.21%	NA
Aus	269	0.00%	0.00%	0.00%	100.00%	NA
Indica I	595	4.20%	2.90%	0.00%	92.94%	NA
Indica II	465	3.90%	0.40%	0.22%	95.48%	NA
Indica III	913	7.30%	0.10%	0.00%	92.55%	NA
Indica Intermediate	786	17.30%	1.70%	0.25%	80.79%	NA
Temperate Japonica	767	61.10%	17.10%	0.00%	21.77%	NA
Tropical Japonica	504	65.50%	0.40%	0.00%	34.13%	NA
Japonica Intermediate	241	36.50%	2.10%	0.00%	61.41%	NA
VI/Aromatic	96	3.10%	0.00%	0.00%	96.88%	NA
Intermediate	90	23.30%	4.40%	1.11%	71.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105257664	A -> DEL	N	N	silent_mutation	Average:10.91; most accessible tissue: Callus, score: 60.798	N	N	N	N
vg1105257664	A -> G	LOC_Os11g09820.1	upstream_gene_variant ; 2687.0bp to feature; MODIFIER	silent_mutation	Average:10.91; most accessible tissue: Callus, score: 60.798	N	N	N	N
vg1105257664	A -> G	LOC_Os11g09840.1	upstream_gene_variant ; 4486.0bp to feature; MODIFIER	silent_mutation	Average:10.91; most accessible tissue: Callus, score: 60.798	N	N	N	N
vg1105257664	A -> G	LOC_Os11g09830.1	downstream_gene_variant ; 440.0bp to feature; MODIFIER	silent_mutation	Average:10.91; most accessible tissue: Callus, score: 60.798	N	N	N	N
vg1105257664	A -> G	LOC_Os11g09820-LOC_Os11g09830	intergenic_region ; MODIFIER	silent_mutation	Average:10.91; most accessible tissue: Callus, score: 60.798	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1105257664	NA	1.10E-07	mr1364	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
vg1105257664	NA	5.39E-07	mr1443	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
vg1105257664	1.02E-06	2.70E-09	mr1624_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