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Detailed information for vg0517761984:

Variant ID: vg0517761984 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17761984
Reference Allele: A	Alternative Allele: G
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 80. )

Flanking Sequence (100 bp) in Reference Genome:

TATTGTAAAAAATGGAGAAAACAATTGAATAGTACAACGTAAATCGTAGTTGATCAAATTTGATGACAATTTAGCAAACTACCATAAATATTGCACATAT[A/G]
AAAGTAAATTACATTGCATTCCATACCACAGAATCATAGAAACAACTTTTTTTACATCACAAGAAATTAGATAATTGTATTGTTCATGACTTAACATCTA

Reverse complement sequence

TAGATGTTAAGTCATGAACAATACAATTATCTAATTTCTTGTGATGTAAAAAAAGTTGTTTCTATGATTCTGTGGTATGGAATGCAATGTAATTTACTTT[T/C]
ATATGTGCAATATTTATGGTAGTTTGCTAAATTGTCATCAAATTTGATCAACTACGATTTACGTTGTACTATTCAATTGTTTTCTCCATTTTTTACAATA

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	20.70%	16.70%	1.46%	61.19%	NA
All Indica	2759	7.50%	1.70%	1.99%	88.84%	NA
All Japonica	1512	48.90%	41.90%	0.46%	8.66%	NA
Aus	269	1.90%	0.40%	1.86%	95.91%	NA
Indica I	595	2.00%	2.20%	2.69%	93.11%	NA
Indica II	465	26.00%	1.10%	2.15%	70.75%	NA
Indica III	913	3.20%	1.20%	1.10%	94.52%	NA
Indica Intermediate	786	5.60%	2.30%	2.42%	89.69%	NA
Temperate Japonica	767	25.80%	71.10%	0.52%	2.61%	NA
Tropical Japonica	504	69.40%	9.50%	0.40%	20.63%	NA
Japonica Intermediate	241	79.70%	17.00%	0.41%	2.90%	NA
VI/Aromatic	96	0.00%	88.50%	0.00%	11.46%	NA
Intermediate	90	30.00%	22.20%	2.22%	45.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0517761984	A -> DEL	N	N	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 44.16	N	N	N	N
vg0517761984	A -> G	LOC_Os05g30660.1	upstream_gene_variant ; 2893.0bp to feature; MODIFIER	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 44.16	N	N	N	N
vg0517761984	A -> G	LOC_Os05g30680.1	upstream_gene_variant ; 3728.0bp to feature; MODIFIER	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 44.16	N	N	N	N
vg0517761984	A -> G	LOC_Os05g30670.1	intron_variant ; MODIFIER	silent_mutation	Average:10.191; most accessible tissue: Callus, score: 44.16	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517761984	3.29E-06	3.29E-06	mr1181_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
vg0517761984	1.49E-06	NA	mr1739_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