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Detailed information for vg0507345057:

Variant ID: vg0507345057 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 7345057
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: 345. )

Flanking Sequence (100 bp) in Reference Genome:

TTTGATCAACGGTTGTAAATAGTTGCAGTGCATATAAACATGCTCTCCTTTGATTGATCTATGTTGGATGTTTCTAGTTATACATGAGTTGTACAACTGT[G/A]
TCGTACGTATAGCAGTACTCTTTTAATAATGGATTTGATTATACCTGGCTTCTACATCCACAAGAGATGTACATGGCCAACAATACTTTGGTTGGTTAGG

Reverse complement sequence

CCTAACCAACCAAAGTATTGTTGGCCATGTACATCTCTTGTGGATGTAGAAGCCAGGTATAATCAAATCCATTATTAAAAGAGTACTGCTATACGTACGA[C/T]
ACAGTTGTACAACTCATGTATAACTAGAAACATCCAACATAGATCAATCAAAGGAGAGCATGTTTATATGCACTGCAACTATTTACAACCGTTGATCAAA

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	92.40%	3.90%	3.79%	0.00%	NA
All Indica	2759	90.80%	6.00%	3.26%	0.00%	NA
All Japonica	1512	96.70%	0.50%	2.78%	0.00%	NA
Aus	269	99.60%	0.00%	0.37%	0.00%	NA
Indica I	595	86.90%	6.20%	6.89%	0.00%	NA
Indica II	465	82.80%	13.10%	4.09%	0.00%	NA
Indica III	913	97.90%	1.40%	0.66%	0.00%	NA
Indica Intermediate	786	90.10%	6.90%	3.05%	0.00%	NA
Temperate Japonica	767	95.60%	1.00%	3.39%	0.00%	NA
Tropical Japonica	504	99.40%	0.00%	0.60%	0.00%	NA
Japonica Intermediate	241	94.60%	0.00%	5.39%	0.00%	NA
VI/Aromatic	96	57.30%	0.00%	42.71%	0.00%	NA
Intermediate	90	84.40%	10.00%	5.56%	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
vg0507345057	G -> A	LOC_Os05g12800.1	upstream_gene_variant ; 3688.0bp to feature; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Callus, score: 85.577	N	N	N	N
vg0507345057	G -> A	LOC_Os05g12804.1	downstream_gene_variant ; 4302.0bp to feature; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Callus, score: 85.577	N	N	N	N
vg0507345057	G -> A	LOC_Os05g12800-LOC_Os05g12804	intergenic_region ; MODIFIER	silent_mutation	Average:58.832; most accessible tissue: Callus, score: 85.577	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0507345057	2.16E-06	4.20E-07	mr1768	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
vg0507345057	9.23E-09	NA	mr1593_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
vg0507345057	NA	1.71E-07	mr1707_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