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Detailed information for vg0521875329:

Variant ID: vg0521875329 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 21875329
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.04, others allele: 0.00, population size: 115. )

Flanking Sequence (100 bp) in Reference Genome:

CACTGCGAGCAGCGGTACCGGCCAAGGCCGGTCCTATGATTTTGAGGTCCCTAAGCGAACTCATCGCGATGGGCCCTCTAAACTATATATAAAATTTTAT[G/A]
ATATATAGATAATAATTTTACTTGCAAAACGATAACAAATACATCCATATATTAAATTTAACATGTCTAGTAATTATGAAGAAATAAAAATAACAATATA

Reverse complement sequence

TATATTGTTATTTTTATTTCTTCATAATTACTAGACATGTTAAATTTAATATATGGATGTATTTGTTATCGTTTTGCAAGTAAAATTATTATCTATATAT[C/T]
ATAAAATTTTATATATAGTTTAGAGGGCCCATCGCGATGAGTTCGCTTAGGGACCTCAAAATCATAGGACCGGCCTTGGCCGGTACCGCTGCTCGCAGTG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	58.70%	40.50%	0.70%	0.15%	NA
All Indica	2759	93.40%	5.10%	1.16%	0.25%	NA
All Japonica	1512	1.50%	98.50%	0.00%	0.00%	NA
Aus	269	48.30%	51.30%	0.37%	0.00%	NA
Indica I	595	93.80%	5.20%	0.84%	0.17%	NA
Indica II	465	89.90%	5.80%	3.44%	0.86%	NA
Indica III	913	98.50%	1.50%	0.00%	0.00%	NA
Indica Intermediate	786	89.40%	8.90%	1.40%	0.25%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.40%	98.60%	0.00%	0.00%	NA
Japonica Intermediate	241	2.10%	97.90%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	46.70%	53.30%	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
vg0521875329	G -> DEL	N	N	silent_mutation	Average:38.358; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg0521875329	G -> A	LOC_Os05g37380.1	upstream_gene_variant ; 3655.0bp to feature; MODIFIER	silent_mutation	Average:38.358; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg0521875329	G -> A	LOC_Os05g37390.1	upstream_gene_variant ; 608.0bp to feature; MODIFIER	silent_mutation	Average:38.358; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg0521875329	G -> A	LOC_Os05g37390.2	upstream_gene_variant ; 608.0bp to feature; MODIFIER	silent_mutation	Average:38.358; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N
vg0521875329	G -> A	LOC_Os05g37380-LOC_Os05g37390	intergenic_region ; MODIFIER	silent_mutation	Average:38.358; most accessible tissue: Zhenshan97 flower, score: 71.382	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0521875329	5.47E-08	6.62E-08	mr1270_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
vg0521875329	NA	5.11E-06	mr1668_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