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Detailed information for vg0608132926:

Variant ID: vg0608132926 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 8132926
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 350. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGATCTTATCCACATAAACAAGTATCCAATCAGTAAATACATAGACCATCAGCATGCCAATGAAGGAGAGACGATGCTTCTAGTTTCAAGCATAAAC[C/T]
GGCCAAACCAACACAATTGTGCCATGAAATTCTCAGCAGAAAAGTGCCAGTTCTCAGGGTGATTTCAATAAGAGAAACCTGTCAGATCCTCTCTGAAGTT

Reverse complement sequence

AACTTCAGAGAGGATCTGACAGGTTTCTCTTATTGAAATCACCCTGAGAACTGGCACTTTTCTGCTGAGAATTTCATGGCACAATTGTGTTGGTTTGGCC[G/A]
GTTTATGCTTGAAACTAGAAGCATCGTCTCTCCTTCATTGGCATGCTGATGGTCTATGTATTTACTGATTGGATACTTGTTTATGTGGATAAGATCTTCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	98.30%	0.90%	0.80%	0.00%	NA
All Indica	2759	100.00%	0.00%	0.00%	0.00%	NA
All Japonica	1512	94.80%	2.80%	2.45%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	100.00%	0.00%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	100.00%	0.00%	0.00%	0.00%	NA
Temperate Japonica	767	91.40%	5.00%	3.65%	0.00%	NA
Tropical Japonica	504	99.20%	0.00%	0.79%	0.00%	NA
Japonica Intermediate	241	96.30%	1.70%	2.07%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0608132926	C -> T	LOC_Os06g14470.2	5_prime_UTR_variant ; 516.0bp to feature; MODIFIER	silent_mutation	Average:65.365; most accessible tissue: Callus, score: 80.557	N	N	N	N
vg0608132926	C -> T	LOC_Os06g14460.1	downstream_gene_variant ; 3546.0bp to feature; MODIFIER	silent_mutation	Average:65.365; most accessible tissue: Callus, score: 80.557	N	N	N	N
vg0608132926	C -> T	LOC_Os06g14470.1	intron_variant ; MODIFIER	silent_mutation	Average:65.365; most accessible tissue: Callus, score: 80.557	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0608132926	3.76E-08	3.61E-11	mr1549_2	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
vg0608132926	3.24E-06	1.17E-09	mr1757_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