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Detailed information for vg0502724894:

Variant ID: vg0502724894 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 2724894
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TGCCTCAACACTGAAACTCTGATGTATGTTATTAGATAGTCCGTAAGCTAAAAAAAACACAGATATTAGAGAAAGACCTAATATCAAATAATTAGGAGGG[G/A]
CGAGGCTTCAAACCCAAGTCGTGCCCACCACCTTGTGGAGCTAGCTGGAAGATCTTGGAACGTTTCTCAGTCTTTGAGCTATACTACCCAAGCCAATGGT

Reverse complement sequence

ACCATTGGCTTGGGTAGTATAGCTCAAAGACTGAGAAACGTTCCAAGATCTTCCAGCTAGCTCCACAAGGTGGTGGGCACGACTTGGGTTTGAAGCCTCG[C/T]
CCCTCCTAATTATTTGATATTAGGTCTTTCTCTAATATCTGTGTTTTTTTTAGCTTACGGACTATCTAATAACATACATCAGAGTTTCAGTGTTGAGGCA

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	71.20%	28.10%	0.19%	0.47%	NA
All Indica	2759	54.50%	44.40%	0.25%	0.80%	NA
All Japonica	1512	98.80%	1.20%	0.00%	0.00%	NA
Aus	269	76.60%	23.00%	0.37%	0.00%	NA
Indica I	595	55.30%	43.70%	0.17%	0.84%	NA
Indica II	465	46.20%	52.00%	0.43%	1.29%	NA
Indica III	913	55.30%	44.20%	0.00%	0.44%	NA
Indica Intermediate	786	58.00%	40.60%	0.51%	0.89%	NA
Temperate Japonica	767	98.30%	1.70%	0.00%	0.00%	NA
Tropical Japonica	504	99.60%	0.40%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	92.70%	7.30%	0.00%	0.00%	NA
Intermediate	90	81.10%	17.80%	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
vg0502724894	G -> DEL	N	N	silent_mutation	Average:69.672; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0502724894	G -> A	LOC_Os05g05470.1	upstream_gene_variant ; 1448.0bp to feature; MODIFIER	silent_mutation	Average:69.672; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0502724894	G -> A	LOC_Os05g05480.1	upstream_gene_variant ; 801.0bp to feature; MODIFIER	silent_mutation	Average:69.672; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0502724894	G -> A	LOC_Os05g05480.2	upstream_gene_variant ; 801.0bp to feature; MODIFIER	silent_mutation	Average:69.672; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N
vg0502724894	G -> A	LOC_Os05g05470-LOC_Os05g05480	intergenic_region ; MODIFIER	silent_mutation	Average:69.672; most accessible tissue: Zhenshan97 panicle, score: 83.904	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0502724894	NA	5.74E-07	mr1925_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
vg0502724894	3.47E-06	5.62E-06	mr1944_2	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