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Detailed information for vg0129748799:

Variant ID: vg0129748799 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 29748799
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 100. )

Flanking Sequence (100 bp) in Reference Genome:

ATAGGATCAACATGCTCAAAGGATTGTGTTTAGGATCTGTGTGACTTGCCTTGCAATAATCGGTCTTCAATTAATCTTCTTGATCACTTCCGGCGCACTC[G/A]
CGAACCTTCGCAACGACGGAAACGACAAGCTAACACGCAAAATGAAGAAAAAGACTAATAAAAACCAAATAAACAATACATGAAAAGTAAACAAACATGT

Reverse complement sequence

ACATGTTTGTTTACTTTTCATGTATTGTTTATTTGGTTTTTATTAGTCTTTTTCTTCATTTTGCGTGTTAGCTTGTCGTTTCCGTCGTTGCGAAGGTTCG[C/T]
GAGTGCGCCGGAAGTGATCAAGAAGATTAATTGAAGACCGATTATTGCAAGGCAAGTCACACAGATCCTAAACACAATCCTTTGAGCATGTTGATCCTAT

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	74.50%	9.10%	14.05%	2.26%	NA
All Indica	2759	58.30%	14.60%	23.38%	3.73%	NA
All Japonica	1512	97.90%	1.30%	0.73%	0.13%	NA
Aus	269	97.80%	2.20%	0.00%	0.00%	NA
Indica I	595	59.30%	6.70%	31.43%	2.52%	NA
Indica II	465	45.40%	20.20%	25.59%	8.82%	NA
Indica III	913	60.50%	19.10%	17.74%	2.74%	NA
Indica Intermediate	786	62.60%	12.10%	22.52%	2.80%	NA
Temperate Japonica	767	99.90%	0.00%	0.13%	0.00%	NA
Tropical Japonica	504	94.00%	3.80%	1.79%	0.40%	NA
Japonica Intermediate	241	99.60%	0.00%	0.41%	0.00%	NA
VI/Aromatic	96	99.00%	0.00%	1.04%	0.00%	NA
Intermediate	90	85.60%	4.40%	7.78%	2.22%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0129748799	G -> A	LOC_Os01g51730.1	downstream_gene_variant ; 4428.0bp to feature; MODIFIER	silent_mutation	Average:10.223; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0129748799	G -> A	LOC_Os01g51735.1	downstream_gene_variant ; 1994.0bp to feature; MODIFIER	silent_mutation	Average:10.223; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0129748799	G -> A	LOC_Os01g51730-LOC_Os01g51735	intergenic_region ; MODIFIER	silent_mutation	Average:10.223; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N
vg0129748799	G -> DEL	N	N	silent_mutation	Average:10.223; most accessible tissue: Zhenshan97 panicle, score: 16.188	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0129748799	2.32E-07	NA	mr1260_2	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