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Detailed information for vg0226811642:

Variant ID: vg0226811642 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26811642
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CATGATTAATACTTTATGCGTGACTTGTTTTTTTAATTTTTTTTATAATTTTTTCAAATAAGACGGACGGTCAAACGTTGGACACGGAAATTCAGGGTTT[G/A]
TCTTTTTTTTTTGGGACAGAGGGAGTAGCTTGCTTAAAGTGAGTGTTTTACTTATGACTAATGCAGTTCGTGGTACAACACAAAGAGGTACTTTTGCGTG

Reverse complement sequence

CACGCAAAAGTACCTCTTTGTGTTGTACCACGAACTGCATTAGTCATAAGTAAAACACTCACTTTAAGCAAGCTACTCCCTCTGTCCCAAAAAAAAAAGA[C/T]
AAACCCTGAATTTCCGTGTCCAACGTTTGACCGTCCGTCTTATTTGAAAAAATTATAAAAAAAATTAAAAAAACAAGTCACGCATAAAGTATTAATCATG

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	88.20%	7.80%	3.05%	1.04%	NA
All Indica	2759	87.70%	8.70%	2.54%	1.05%	NA
All Japonica	1512	92.80%	1.20%	4.70%	1.32%	NA
Aus	269	60.20%	39.80%	0.00%	0.00%	NA
Indica I	595	89.90%	6.10%	3.87%	0.17%	NA
Indica II	465	78.90%	18.70%	1.94%	0.43%	NA
Indica III	913	89.40%	6.80%	1.53%	2.30%	NA
Indica Intermediate	786	89.40%	6.90%	3.05%	0.64%	NA
Temperate Japonica	767	94.90%	2.20%	2.87%	0.00%	NA
Tropical Japonica	504	87.10%	0.20%	8.93%	3.77%	NA
Japonica Intermediate	241	97.90%	0.00%	1.66%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	93.30%	3.30%	3.33%	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
vg0226811642	G -> A	LOC_Os02g44320.1	upstream_gene_variant ; 2914.0bp to feature; MODIFIER	silent_mutation	Average:48.599; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0226811642	G -> A	LOC_Os02g44310-LOC_Os02g44320	intergenic_region ; MODIFIER	silent_mutation	Average:48.599; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N
vg0226811642	G -> DEL	N	N	silent_mutation	Average:48.599; most accessible tissue: Minghui63 panicle, score: 75.788	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0226811642	NA	5.09E-07	mr1278	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
vg0226811642	4.07E-07	4.94E-07	mr1312	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
vg0226811642	NA	5.71E-06	mr1619	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
vg0226811642	NA	7.65E-07	mr1962	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
vg0226811642	5.19E-06	5.18E-06	mr1919_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