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Detailed information for vg1208264724:

Variant ID: vg1208264724 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 8264724
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.96, A: 0.02, others allele: 0.00, population size: 45. )

Flanking Sequence (100 bp) in Reference Genome:

TATAGGTATGTTTTTTTTTAAAAAAAAGGGCACCTATTCCTTTTACCACAAAGATGCTTGTTCTTGGGTAGGCCCCGTGCCAACTACTCCGATGGGACGG[G/A]
TCCTAAAAGGTGCCGGATTTTTAATAAAAACCGGCATATTTCTTTGAGACCAATAGTTGGTGCTCTATTTGAGGATAAAGGTGCCGATTCTTTGGATTTT

Reverse complement sequence

AAAATCCAAAGAATCGGCACCTTTATCCTCAAATAGAGCACCAACTATTGGTCTCAAAGAAATATGCCGGTTTTTATTAAAAATCCGGCACCTTTTAGGA[C/T]
CCGTCCCATCGGAGTAGTTGGCACGGGGCCTACCCAAGAACAAGCATCTTTGTGGTAAAAGGAATAGGTGCCCTTTTTTTTAAAAAAAAACATACCTATA

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	38.70%	26.70%	0.57%	34.05%	NA
All Indica	2759	6.00%	44.10%	0.87%	49.00%	NA
All Japonica	1512	94.40%	1.30%	0.20%	4.10%	NA
Aus	269	46.50%	1.90%	0.00%	51.67%	NA
Indica I	595	6.90%	29.90%	0.67%	62.52%	NA
Indica II	465	6.00%	37.80%	1.08%	55.05%	NA
Indica III	913	3.40%	57.80%	0.66%	38.12%	NA
Indica Intermediate	786	8.30%	42.70%	1.15%	47.84%	NA
Temperate Japonica	767	92.40%	0.70%	0.39%	6.52%	NA
Tropical Japonica	504	95.80%	3.00%	0.00%	1.19%	NA
Japonica Intermediate	241	97.50%	0.00%	0.00%	2.49%	NA
VI/Aromatic	96	54.20%	2.10%	0.00%	43.75%	NA
Intermediate	90	66.70%	17.80%	0.00%	15.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1208264724	G -> DEL	N	N	silent_mutation	Average:43.741; most accessible tissue: Callus, score: 83.42	N	N	N	N
vg1208264724	G -> A	LOC_Os12g14480.1	downstream_gene_variant ; 1589.0bp to feature; MODIFIER	silent_mutation	Average:43.741; most accessible tissue: Callus, score: 83.42	N	N	N	N
vg1208264724	G -> A	LOC_Os12g14470-LOC_Os12g14480	intergenic_region ; MODIFIER	silent_mutation	Average:43.741; most accessible tissue: Callus, score: 83.42	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1208264724	3.48E-06	3.48E-06	mr1473	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
vg1208264724	NA	5.06E-07	mr1302_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
vg1208264724	NA	1.52E-24	mr1350_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
vg1208264724	NA	1.43E-06	mr1418_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
vg1208264724	NA	1.69E-09	mr1506_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
vg1208264724	NA	5.70E-08	mr1604_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
vg1208264724	NA	1.13E-07	mr1824_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