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Detailed information for vg0917477265:

Variant ID: vg0917477265 (JBrowse)	Variation Type: SNP
Chromosome: chr09	Position: 17477265
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 236. )

Flanking Sequence (100 bp) in Reference Genome:

CCATTTCTTTTATGCAGATGTAATTGTTCAACAGTTGCTCAGGTTTTTCAGCATTTCTTTCTGCATCGAATATTCCGAATTCATTTTTGATACGGCTGGA[A/C]
CAGCCATAACAATTATTCTGCTAATTGAGAAAATCTGATTGTTATGTCCCATCTATAGATGGTGAATTGAATGTTGTGGTACCACCAAAAATAAACTTGG

Reverse complement sequence

CCAAGTTTATTTTTGGTGGTACCACAACATTCAATTCACCATCTATAGATGGGACATAACAATCAGATTTTCTCAATTAGCAGAATAATTGTTATGGCTG[T/G]
TCCAGCCGTATCAAAAATGAATTCGGAATATTCGATGCAGAAAGAAATGCTGAAAAACCTGAGCAACTGTTGAACAATTACATCTGCATAAAAGAAATGG

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	99.70%	0.30%	0.02%	0.00%	NA
All Indica	2759	99.50%	0.50%	0.04%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	98.50%	1.30%	0.17%	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	99.60%	0.40%	0.00%	0.00%	NA
Temperate Japonica	767	99.90%	0.10%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	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
vg0917477265	A -> C	LOC_Os09g28780.1	upstream_gene_variant ; 4188.0bp to feature; MODIFIER	N	Average:43.164; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg0917477265	A -> C	LOC_Os09g28760.1	downstream_gene_variant ; 3774.0bp to feature; MODIFIER	N	Average:43.164; most accessible tissue: Callus, score: 70.108	N	N	N	N
vg0917477265	A -> C	LOC_Os09g28770.1	intron_variant ; MODIFIER	N	Average:43.164; most accessible tissue: Callus, score: 70.108	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0917477265	4.28E-06	1.56E-07	mr1261	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