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Detailed information for vg1223038282:

Variant ID: vg1223038282 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 23038282
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

AATGCAAAAAAGCTAAAGGAAACAAGACTCCAGAAATACCCATTAAAACGACTATAAAAGAAGAAGGGTATTCTAAAAAACCCACATACAAGGAATGCCT[A/G]
ACAAAAGGAGTGGATCCATTAGATGGGGAATATATTGATTAGAAAATAATAGAAAATTTTGAAGAAGCCTCCCCACAATTAAAGAAGGAATTAAAGGAAG

Reverse complement sequence

CTTCCTTTAATTCCTTCTTTAATTGTGGGGAGGCTTCTTCAAAATTTTCTATTATTTTCTAATCAATATATTCCCCATCTAATGGATCCACTCCTTTTGT[T/C]
AGGCATTCCTTGTATGTGGGTTTTTTAGAATACCCTTCTTCTTTTATAGTCGTTTTAATGGGTATTTCTGGAGTCTTGTTTCCTTTAGCTTTTTTGCATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	97.40%	0.70%	1.97%	0.00%	NA
All Indica	2759	95.70%	1.10%	3.26%	0.00%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.40%	0.00%	0.00%	NA
Indica I	595	94.80%	1.00%	4.20%	0.00%	NA
Indica II	465	89.00%	0.90%	10.11%	0.00%	NA
Indica III	913	98.70%	1.00%	0.33%	0.00%	NA
Indica Intermediate	786	96.70%	1.40%	1.91%	0.00%	NA
Temperate Japonica	767	99.70%	0.10%	0.13%	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	97.80%	0.00%	2.22%	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
vg1223038282	A -> G	LOC_Os12g37540.1	synonymous_variant ; p.Leu235Leu; LOW	synonymous_codon	Average:11.809; most accessible tissue: Callus, score: 20.099	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1223038282	5.11E-06	6.24E-06	mr1706	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