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Detailed information for vg0611102764:

Variant ID: vg0611102764 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 11102764
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.60, T: 0.40, others allele: 0.00, population size: 97. )

Flanking Sequence (100 bp) in Reference Genome:

ACGAGAATAGTCATGTAACCAGGTTTTTCCCTATGGACCAGCATCCGGACATACGCACGCAATCTTTCCGTATATATTATAAATCGAATTGATTTTTTTA[T/A]
TTTTTATTTGAAATTTTAATCAAACTTATAGAAAAATATAACAACACTTATAGCACGAAATTAATTAGTTTTATTACATCTAACATTGAACATATTTTGA

Reverse complement sequence

TCAAAATATGTTCAATGTTAGATGTAATAAAACTAATTAATTTCGTGCTATAAGTGTTGTTATATTTTTCTATAAGTTTGATTAAAATTTCAAATAAAAA[A/T]
TAAAAAAATCAATTCGATTTATAATATATACGGAAAGATTGCGTGCGTATGTCCGGATGCTGGTCCATAGGGAAAAACCTGGTTACATGACTATTCTCGT

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	62.80%	36.90%	0.36%	0.00%	NA
All Indica	2759	47.80%	51.80%	0.36%	0.00%	NA
All Japonica	1512	84.90%	14.70%	0.40%	0.00%	NA
Aus	269	78.10%	21.90%	0.00%	0.00%	NA
Indica I	595	20.30%	79.20%	0.50%	0.00%	NA
Indica II	465	89.20%	10.50%	0.22%	0.00%	NA
Indica III	913	40.20%	59.80%	0.00%	0.00%	NA
Indica Intermediate	786	53.10%	46.20%	0.76%	0.00%	NA
Temperate Japonica	767	84.00%	15.40%	0.65%	0.00%	NA
Tropical Japonica	504	87.70%	12.30%	0.00%	0.00%	NA
Japonica Intermediate	241	82.20%	17.40%	0.41%	0.00%	NA
VI/Aromatic	96	88.50%	11.50%	0.00%	0.00%	NA
Intermediate	90	74.40%	24.40%	1.11%	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
vg0611102764	T -> A	LOC_Os06g19490.1	upstream_gene_variant ; 1471.0bp to feature; MODIFIER	silent_mutation	Average:41.092; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0611102764	T -> A	LOC_Os06g19500.1	downstream_gene_variant ; 244.0bp to feature; MODIFIER	silent_mutation	Average:41.092; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N
vg0611102764	T -> A	LOC_Os06g19490-LOC_Os06g19500	intergenic_region ; MODIFIER	silent_mutation	Average:41.092; most accessible tissue: Zhenshan97 panicle, score: 77.482	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0611102764	NA	3.27E-06	mr1857	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
vg0611102764	NA	9.56E-07	mr1931_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
vg0611102764	1.69E-06	1.69E-06	mr1971_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