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Detailed information for vg0318761133:

Variant ID: vg0318761133 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 18761133
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: 241. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAGGTAGTCAGTGCAGCTTTTTGACGAACCACTTCAAGGTTTCACTGAAAGGCAGCAGGCCAAAGGACCTCAGTTCTCTAGCCGGAAAGAAGTAGGCC[G/A]
AAAGGTGATTGATAAAGGATAATCAGAAGCATGCTTTGCATCACTCGAGGAAGACCCCTGATCACCCTGCAATAGTCACCTTGTCATTGAGGTAGAAAAA

Reverse complement sequence

TTTTTCTACCTCAATGACAAGGTGACTATTGCAGGGTGATCAGGGGTCTTCCTCGAGTGATGCAAAGCATGCTTCTGATTATCCTTTATCAATCACCTTT[C/T]
GGCCTACTTCTTTCCGGCTAGAGAACTGAGGTCCTTTGGCCTGCTGCCTTTCAGTGAAACCTTGAAGTGGTTCGTCAAAAAGCTGCACTGACTACCTTCA

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	95.50%	1.80%	2.31%	0.40%	NA
All Indica	2759	99.90%	0.00%	0.11%	0.00%	NA
All Japonica	1512	86.40%	5.60%	6.88%	1.12%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.80%	0.00%	0.22%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.00%	0.25%	0.00%	NA
Temperate Japonica	767	83.60%	5.30%	11.08%	0.00%	NA
Tropical Japonica	504	91.50%	6.70%	1.59%	0.20%	NA
Japonica Intermediate	241	84.60%	4.10%	4.56%	6.64%	NA
VI/Aromatic	96	96.90%	0.00%	1.04%	2.08%	NA
Intermediate	90	97.80%	1.10%	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
vg0318761133	G -> A	LOC_Os03g32770.1	downstream_gene_variant ; 691.0bp to feature; MODIFIER	silent_mutation	Average:33.692; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0318761133	G -> A	LOC_Os03g32780.1	downstream_gene_variant ; 1840.0bp to feature; MODIFIER	silent_mutation	Average:33.692; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0318761133	G -> A	LOC_Os03g32770-LOC_Os03g32780	intergenic_region ; MODIFIER	silent_mutation	Average:33.692; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N
vg0318761133	G -> DEL	N	N	silent_mutation	Average:33.692; most accessible tissue: Zhenshan97 panicle, score: 54.901	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0318761133	7.90E-07	7.90E-07	mr1881	Jap_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