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Detailed information for vg0601745967:

Variant ID: vg0601745967 (JBrowse)	Variation Type: SNP
Chromosome: chr06	Position: 1745967
Reference Allele: T	Alternative Allele: A
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.99, A: 0.02, others allele: 0.00, population size: 218. )

Flanking Sequence (100 bp) in Reference Genome:

TAGATACTTATTTGCTATTGCAAGTTTGAATTAAATATGCATTTTGCATAGTTGTAGTGGACCCTTTGTTTTTAGCCAAGTTTTCTATACCAGCTCAAGG[T/A]
TAAGTGGAATCGCTATGCCGATTAAAATGTCATGGGTTGTTGGTCTTGGCAATGGACTCGGTAACCAAGCTCCTAGCAAGAGTGGCTAGCAAGGACATTA

Reverse complement sequence

TAATGTCCTTGCTAGCCACTCTTGCTAGGAGCTTGGTTACCGAGTCCATTGCCAAGACCAACAACCCATGACATTTTAATCGGCATAGCGATTCCACTTA[A/T]
CCTTGAGCTGGTATAGAAAACTTGGCTAAAAACAAAGGGTCCACTACAACTATGCAAAATGCATATTTAATTCAAACTTGCAATAGCAAATAAGTATCTA

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	85.00%	14.70%	0.30%	0.00%	NA
All Indica	2759	81.30%	18.20%	0.51%	0.00%	NA
All Japonica	1512	99.80%	0.20%	0.00%	0.00%	NA
Aus	269	39.40%	60.60%	0.00%	0.00%	NA
Indica I	595	89.60%	8.60%	1.85%	0.00%	NA
Indica II	465	90.50%	9.20%	0.22%	0.00%	NA
Indica III	913	73.40%	26.60%	0.00%	0.00%	NA
Indica Intermediate	786	78.60%	21.10%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.80%	0.00%	0.00%	NA
VI/Aromatic	96	87.50%	12.50%	0.00%	0.00%	NA
Intermediate	90	86.70%	13.30%	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
vg0601745967	T -> A	LOC_Os06g04169.1	upstream_gene_variant ; 3386.0bp to feature; MODIFIER	silent_mutation	Average:44.258; most accessible tissue: Minghui63 root, score: 59.984	N	N	N	N
vg0601745967	T -> A	LOC_Os06g04169.2	upstream_gene_variant ; 3390.0bp to feature; MODIFIER	silent_mutation	Average:44.258; most accessible tissue: Minghui63 root, score: 59.984	N	N	N	N
vg0601745967	T -> A	LOC_Os06g04169-LOC_Os06g04190	intergenic_region ; MODIFIER	silent_mutation	Average:44.258; most accessible tissue: Minghui63 root, score: 59.984	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0601745967	NA	5.54E-08	mr1627	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
vg0601745967	NA	3.10E-06	mr1977	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