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Detailed information for vg1200522212:

Variant ID: vg1200522212 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 522212
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

CCACGTGGAGGCGCTCGCGGCGCAGGCCGGCGGCGCCGTTCTTGCAGTAGAGGGCACGGAGCTCGGCGACGTCGGCGGCGCGCCATCGGAGGAGGAGCGC[G/A]
AGGTGGTGGCAGAGCTTGGGATGCTGGTAGACGCACATGATGGTGAAGAGCGCGTTGAGCATCTGGTTGGCCACCTCGGTCCATCGGCGGCGGCGCGAGG

Reverse complement sequence

CCTCGCGCCGCCGCCGATGGACCGAGGTGGCCAACCAGATGCTCAACGCGCTCTTCACCATCATGTGCGTCTACCAGCATCCCAAGCTCTGCCACCACCT[C/T]
GCGCTCCTCCTCCGATGGCGCGCCGCCGACGTCGCCGAGCTCCGTGCCCTCTACTGCAAGAACGGCGCCGCCGGCCTGCGCCGCGAGCGCCTCCACGTGG

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	90.40%	9.40%	0.19%	0.00%	NA
All Indica	2759	83.90%	15.70%	0.33%	0.00%	NA
All Japonica	1512	99.50%	0.50%	0.00%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	56.80%	42.70%	0.50%	0.00%	NA
Indica II	465	96.80%	3.20%	0.00%	0.00%	NA
Indica III	913	97.00%	3.00%	0.00%	0.00%	NA
Indica Intermediate	786	81.70%	17.60%	0.76%	0.00%	NA
Temperate Japonica	767	99.10%	0.90%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	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%	2.20%	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
vg1200522212	G -> A	LOC_Os12g01890.1	synonymous_variant ; p.Leu157Leu; LOW	synonymous_codon	Average:69.426; most accessible tissue: Zhenshan97 flower, score: 81.855	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1200522212	NA	1.70E-06	mr1389	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
vg1200522212	NA	2.60E-07	mr1729	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
vg1200522212	NA	1.49E-07	mr1729	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