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Detailed information for vg1212567284:

Variant ID: vg1212567284 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 12567284
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.93, A: 0.07, others allele: 0.00, population size: 70. )

Flanking Sequence (100 bp) in Reference Genome:

CTGGGCCCATCTTGCTCCCTCCCTGGCGCCCTTCTGCACCTTCGCCTGGTCTGCCGGCCAGCGCCCTCCCGTAGACCCAGCATCCGGCGCCGATTTGGGG[G/A]
ATTTTTTGGAAAAAAATGGGGTTTTGGGTGGACGGAAAGACACGAGAGAAAAGGAGGGAAATCGAATCGATTTCCGATGGCGGCGGCGCCGATTGTGGCT

Reverse complement sequence

AGCCACAATCGGCGCCGCCGCCATCGGAAATCGATTCGATTTCCCTCCTTTTCTCTCGTGTCTTTCCGTCCACCCAAAACCCCATTTTTTTCCAAAAAAT[C/T]
CCCCAAATCGGCGCCGGATGCTGGGTCTACGGGAGGGCGCTGGCCGGCAGACCAGGCGAAGGTGCAGAAGGGCGCCAGGGAGGGAGCAAGATGGGCCCAG

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	93.20%	3.60%	2.12%	1.12%	NA
All Indica	2759	90.50%	4.20%	3.41%	1.88%	NA
All Japonica	1512	96.80%	2.90%	0.20%	0.07%	NA
Aus	269	97.00%	2.60%	0.37%	0.00%	NA
Indica I	595	89.70%	2.90%	6.39%	1.01%	NA
Indica II	465	82.40%	13.10%	3.23%	1.29%	NA
Indica III	913	94.30%	0.80%	1.86%	3.07%	NA
Indica Intermediate	786	91.30%	4.10%	3.05%	1.53%	NA
Temperate Japonica	767	94.30%	5.30%	0.39%	0.00%	NA
Tropical Japonica	504	99.40%	0.40%	0.00%	0.20%	NA
Japonica Intermediate	241	99.60%	0.40%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	95.60%	2.20%	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
vg1212567284	G -> DEL	N	N	silent_mutation	Average:61.693; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg1212567284	G -> A	LOC_Os12g22284.1	downstream_gene_variant ; 1473.0bp to feature; MODIFIER	silent_mutation	Average:61.693; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N
vg1212567284	G -> A	LOC_Os12g22270-LOC_Os12g22284	intergenic_region ; MODIFIER	silent_mutation	Average:61.693; most accessible tissue: Zhenshan97 young leaf, score: 81.102	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1212567284	NA	4.21E-06	mr1153_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
vg1212567284	NA	1.19E-10	mr1228_2	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
vg1212567284	NA	7.40E-07	mr1275_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
vg1212567284	NA	3.81E-06	mr1407_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
vg1212567284	NA	1.82E-07	mr1607_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
vg1212567284	3.10E-06	NA	mr1852_2	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
vg1212567284	NA	7.10E-09	mr1940_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