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Detailed information for vg0421348658:

Variant ID: vg0421348658 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21348658
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, A: 0.05, others allele: 0.00, population size: 112. )

Flanking Sequence (100 bp) in Reference Genome:

ATACATTGATTAATGCATAAATCTAGTAGAAAAGGAACGGAGGGAGTATTGCACGTACCGGCAATTTTTCTTTCAGAAAACCTACACCACGGCATCCCGT[G/A]
GAGACGGGATCCCCTCCTCCTACCTCACTCCTCTCCCCCAAATCATCTGGATCCCCTCCTCCTACCTCACTCTCCTCCCCCAAATCAGACGGCACTGTAG

Reverse complement sequence

CTACAGTGCCGTCTGATTTGGGGGAGGAGAGTGAGGTAGGAGGAGGGGATCCAGATGATTTGGGGGAGAGGAGTGAGGTAGGAGGAGGGGATCCCGTCTC[C/T]
ACGGGATGCCGTGGTGTAGGTTTTCTGAAAGAAAAATTGCCGGTACGTGCAATACTCCCTCCGTTCCTTTTCTACTAGATTTATGCATTAATCAATGTAT

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	85.00%	15.00%	0.00%	0.00%	NA
All Indica	2759	76.70%	23.30%	0.00%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	79.60%	20.40%	0.00%	0.00%	NA
Indica I	595	77.80%	22.20%	0.00%	0.00%	NA
Indica II	465	79.60%	20.40%	0.00%	0.00%	NA
Indica III	913	73.80%	26.20%	0.00%	0.00%	NA
Indica Intermediate	786	77.60%	22.40%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	95.80%	4.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	8.90%	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
vg0421348658	G -> A	LOC_Os04g35130.1	upstream_gene_variant ; 1126.0bp to feature; MODIFIER	silent_mutation	Average:60.672; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0421348658	G -> A	LOC_Os04g35114.1	downstream_gene_variant ; 4081.0bp to feature; MODIFIER	silent_mutation	Average:60.672; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N
vg0421348658	G -> A	LOC_Os04g35114-LOC_Os04g35130	intergenic_region ; MODIFIER	silent_mutation	Average:60.672; most accessible tissue: Minghui63 panicle, score: 82.128	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421348658	1.87E-06	NA	mr1719	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
vg0421348658	2.64E-06	2.64E-06	mr1267_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