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Detailed information for vg0230907885:

Variant ID: vg0230907885 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 30907885
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: 0.01, others allele: 0.00, population size: 126. )

Flanking Sequence (100 bp) in Reference Genome:

TGTAAGATTGTGAGATTAGATGAGAGTGTAGGAGTGTTTTGGAGATGGCTTGAAGATTAGGTTTGACTGAGCACTTTGGATATCTTGTGGGCTGTCACTT[G/A]
GGCTTATTACTCTTGGAGATCTTCTCCTAGACGGTTAGGTGTTGCCCGTGACTTCCAAATATCTTGTGGATATCCCGGGAAAGTTTGTGAAGGTTTTCCT

Reverse complement sequence

AGGAAAACCTTCACAAACTTTCCCGGGATATCCACAAGATATTTGGAAGTCACGGGCAACACCTAACCGTCTAGGAGAAGATCTCCAAGAGTAATAAGCC[C/T]
AAGTGACAGCCCACAAGATATCCAAAGTGCTCAGTCAAACCTAATCTTCAAGCCATCTCCAAAACACTCCTACACTCTCATCTAATCTCACAATCTTACA

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	90.00%	10.00%	0.00%	0.00%	NA
All Indica	2759	83.60%	16.40%	0.00%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	95.20%	4.80%	0.00%	0.00%	NA
Indica I	595	95.30%	4.70%	0.00%	0.00%	NA
Indica II	465	57.60%	42.40%	0.00%	0.00%	NA
Indica III	913	92.70%	7.30%	0.00%	0.00%	NA
Indica Intermediate	786	79.50%	20.50%	0.00%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	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	93.30%	6.70%	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
vg0230907885	G -> A	LOC_Os02g50610.1	intron_variant ; MODIFIER	silent_mutation	Average:20.411; most accessible tissue: Zhenshan97 flag leaf, score: 38.066	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0230907885	2.65E-06	8.98E-06	mr1922	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
vg0230907885	NA	6.34E-06	mr1971_2	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