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Detailed information for vg0423532668:

Variant ID: vg0423532668 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 23532668
Reference Allele: C	Alternative Allele: A
Primary Allele: C	Secondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.01, others allele: 0.00, population size: 259. )

Flanking Sequence (100 bp) in Reference Genome:

TGTGGCAGCTCAGTGCGAATGTAAAATCTGCAGGTTAATTTTGTTTTGGATAATTTGGGGTATCAACTTGGCTACTTGATATGGTGTTGACAATAATGCT[C/A]
AGATCAGGATAACTGATCTTGCATACTGTTTTCGTTGTGGTTGCTTCGGAAAAAAAAGTTTTGATTTTTTTCTTTCAGAGATTTCATATAGCTGCGGCTG

Reverse complement sequence

CAGCCGCAGCTATATGAAATCTCTGAAAGAAAAAAATCAAAACTTTTTTTTCCGAAGCAACCACAACGAAAACAGTATGCAAGATCAGTTATCCTGATCT[G/T]
AGCATTATTGTCAACACCATATCAAGTAGCCAAGTTGATACCCCAAATTATCCAAAACAAAATTAACCTGCAGATTTTACATTCGCACTGAGCTGCCACA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.70%	2.20%	0.04%	0.00%	NA
All Indica	2759	99.90%	0.10%	0.00%	0.00%	NA
All Japonica	1512	93.40%	6.50%	0.13%	0.00%	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	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	100.00%	0.00%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	97.80%	2.00%	0.26%	0.00%	NA
Tropical Japonica	504	94.00%	6.00%	0.00%	0.00%	NA
Japonica Intermediate	241	78.00%	22.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	4.40%	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
vg0423532668	C -> A	LOC_Os04g39520.1	downstream_gene_variant ; 307.0bp to feature; MODIFIER	silent_mutation	Average:48.311; most accessible tissue: Callus, score: 85.751	N	N	N	N
vg0423532668	C -> A	LOC_Os04g39530.1	downstream_gene_variant ; 2754.0bp to feature; MODIFIER	silent_mutation	Average:48.311; most accessible tissue: Callus, score: 85.751	N	N	N	N
vg0423532668	C -> A	LOC_Os04g39520-LOC_Os04g39530	intergenic_region ; MODIFIER	silent_mutation	Average:48.311; most accessible tissue: Callus, score: 85.751	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0423532668	8.37E-07	3.12E-07	mr1768	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