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Detailed information for vg0614574227:

Variant ID: vg0614574227 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 14574227
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 1.01, others allele: 0.00, population size: 313. )

Flanking Sequence (100 bp) in Reference Genome:

CAATGGAAAGCCAAAAGTTCAAAAGAAAAGGTCAACACAGCTTAGTAGAACTACCTGTTGGCAACTTTTTTGACAAGTTGACAAGCACGATCGCAGCACC[T/A]
TAAGCCTTGCGGTGATCCTAGAGTCGCCAACCACCTCGATCTAGCAAAAAGCTAAACCTAGATGGGTTTTGATAACTAAACCGGCTAGCGGAGCCGATTT

Reverse complement sequence

AAATCGGCTCCGCTAGCCGGTTTAGTTATCAAAACCCATCTAGGTTTAGCTTTTTGCTAGATCGAGGTGGTTGGCGACTCTAGGATCACCGCAAGGCTTA[A/T]
GGTGCTGCGATCGTGCTTGTCAACTTGTCAAAAAAGTTGCCAACAGGTAGTTCTACTAAGCTGTGTTGACCTTTTCTTTTGAACTTTTGGCTTTCCATTG

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	91.30%	7.00%	1.67%	0.00%	NA
All Indica	2759	85.90%	11.40%	2.68%	0.00%	NA
All Japonica	1512	99.10%	0.70%	0.20%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	0.50%	1.01%	0.00%	NA
Indica II	465	88.20%	10.30%	1.51%	0.00%	NA
Indica III	913	75.60%	20.90%	3.50%	0.00%	NA
Indica Intermediate	786	87.00%	9.30%	3.69%	0.00%	NA
Temperate Japonica	767	98.60%	1.20%	0.26%	0.00%	NA
Tropical Japonica	504	99.60%	0.20%	0.20%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	91.10%	7.80%	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
vg0614574227	T -> A	LOC_Os06g24830.1	upstream_gene_variant ; 4538.0bp to feature; MODIFIER	silent_mutation	Average:45.865; most accessible tissue: Zhenshan97 flag leaf, score: 61.926	N	N	N	N
vg0614574227	T -> A	LOC_Os06g24840.1	intron_variant ; MODIFIER	silent_mutation	Average:45.865; most accessible tissue: Zhenshan97 flag leaf, score: 61.926	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0614574227	5.87E-06	NA	mr1094	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