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Detailed information for vg0132054059:

Variant ID: vg0132054059 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 32054059
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: 309. )

Flanking Sequence (100 bp) in Reference Genome:

TTGGAACATCAATGCTCATAGCATTGTCTATATTACTCAAGGTCATGCCGGGTTCAAGTTGTCAACAACAATGGAAAGACAGTGTTTGATGGAGAGGTTC[G/A]
TCCTGGGCAGCTGCTAATTATACCACAACACCATGTAGTTGTGAAAAAAGCACAAAGAGAAGGATGCTTATATATTGCATTCAAAACCAACCCTAATTCC

Reverse complement sequence

GGAATTAGGGTTGGTTTTGAATGCAATATATAAGCATCCTTCTCTTTGTGCTTTTTTCACAACTACATGGTGTTGTGGTATAATTAGCAGCTGCCCAGGA[C/T]
GAACCTCTCCATCAAACACTGTCTTTCCATTGTTGTTGACAACTTGAACCCGGCATGACCTTGAGTAATATAGACAATGCTATGAGCATTGATGTTCCAA

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	96.80%	3.20%	0.00%	0.00%	NA
All Indica	2759	94.60%	5.40%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	83.00%	17.00%	0.00%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	99.90%	0.10%	0.00%	0.00%	NA
Indica Intermediate	786	96.10%	3.90%	0.00%	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	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg0132054059	G -> A	LOC_Os01g55630.1	splice_region_variant&intron_variant ; LOW	silent_mutation	Average:45.386; most accessible tissue: Callus, score: 84.144	N	N	N	N
vg0132054059	G -> A	LOC_Os01g55620.1	upstream_gene_variant ; 3293.0bp to feature; MODIFIER	silent_mutation	Average:45.386; most accessible tissue: Callus, score: 84.144	N	N	N	N
vg0132054059	G -> A	LOC_Os01g55640.1	upstream_gene_variant ; 3096.0bp to feature; MODIFIER	silent_mutation	Average:45.386; most accessible tissue: Callus, score: 84.144	N	N	N	N
vg0132054059	G -> A	LOC_Os01g55650.1	downstream_gene_variant ; 3324.0bp to feature; MODIFIER	silent_mutation	Average:45.386; most accessible tissue: Callus, score: 84.144	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0132054059	7.42E-06	7.40E-06	mr1760_2	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