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Detailed information for vg0529452069:

Variant ID: vg0529452069 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 29452069
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.99, others allele: 0.00, population size: 99. )

Flanking Sequence (100 bp) in Reference Genome:

TAGCTATGAATCTAGACAACTGTTTGTCTAGATTCGTAGCCAAAAGTGGTTATATTTTGGAACAGAGGTAGTAGTTTCAATGGAAATTTTCAAAGAGTTT[G/A]
TAGCTGTTGCTAAGTTTCCTTTAAAATCTACATGTAATGAACCAATCCATAGGAATTTCATAGGATTTGGTAAGCTCCAATCCTTTGAATCAAAGGGTCA

Reverse complement sequence

TGACCCTTTGATTCAAAGGATTGGAGCTTACCAAATCCTATGAAATTCCTATGGATTGGTTCATTACATGTAGATTTTAAAGGAAACTTAGCAACAGCTA[C/T]
AAACTCTTTGAAAATTTCCATTGAAACTACTACCTCTGTTCCAAAATATAACCACTTTTGGCTACGAATCTAGACAAACAGTTGTCTAGATTCATAGCTA

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	94.40%	4.20%	1.44%	0.00%	NA
All Indica	2759	90.70%	6.90%	2.43%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	95.30%	0.20%	4.54%	0.00%	NA
Indica II	465	82.20%	14.60%	3.23%	0.00%	NA
Indica III	913	94.30%	5.40%	0.33%	0.00%	NA
Indica Intermediate	786	88.00%	9.20%	2.80%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	97.90%	2.10%	0.00%	0.00%	NA
Intermediate	90	93.30%	5.60%	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
vg0529452069	G -> A	LOC_Os05g51360.1	upstream_gene_variant ; 3490.0bp to feature; MODIFIER	silent_mutation	Average:39.117; most accessible tissue: Callus, score: 60.472	N	N	N	N
vg0529452069	G -> A	LOC_Os05g51350.1	downstream_gene_variant ; 1519.0bp to feature; MODIFIER	silent_mutation	Average:39.117; most accessible tissue: Callus, score: 60.472	N	N	N	N
vg0529452069	G -> A	LOC_Os05g51350-LOC_Os05g51360	intergenic_region ; MODIFIER	silent_mutation	Average:39.117; most accessible tissue: Callus, score: 60.472	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0529452069	3.76E-06	NA	mr1874	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