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Detailed information for vg1217928334:

Variant ID: vg1217928334 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 17928334
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: 263. )

Flanking Sequence (100 bp) in Reference Genome:

CATGGTTATTAAGAAAGTAGGTAGAAGTGAATGTTGAAGGGTTGTGATTGGATGAGTAGTGGAGGTAGGTGAGAAAAGTGAATGGCGGAGGGTTGTGATT[G/A]
GTTGGGAAGAGAATGTTGGTGGAGAAGTTGTTATATTTTGGGACAAATTCTGAGGGCTAAAAGTTGTTATATTTTGGGAGTTAGGACGGAGGGAGTATTT

Reverse complement sequence

AAATACTCCCTCCGTCCTAACTCCCAAAATATAACAACTTTTAGCCCTCAGAATTTGTCCCAAAATATAACAACTTCTCCACCAACATTCTCTTCCCAAC[C/T]
AATCACAACCCTCCGCCATTCACTTTTCTCACCTACCTCCACTACTCATCCAATCACAACCCTTCAACATTCACTTCTACCTACTTTCTTAATAACCATG

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	96.70%	3.30%	0.02%	0.00%	NA
All Indica	2759	97.50%	2.50%	0.00%	0.00%	NA
All Japonica	1512	98.20%	1.70%	0.07%	0.00%	NA
Aus	269	77.70%	22.30%	0.00%	0.00%	NA
Indica I	595	92.90%	7.10%	0.00%	0.00%	NA
Indica II	465	99.80%	0.20%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	96.90%	3.10%	0.00%	0.00%	NA
Temperate Japonica	767	99.00%	0.90%	0.13%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	92.50%	7.50%	0.00%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	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
vg1217928334	G -> A	LOC_Os12g29990.1	intron_variant ; MODIFIER	silent_mutation	Average:38.989; most accessible tissue: Minghui63 root, score: 59.105	N	N	N	N
vg1217928334	G -> A	LOC_Os12g29990.4	intron_variant ; MODIFIER	silent_mutation	Average:38.989; most accessible tissue: Minghui63 root, score: 59.105	N	N	N	N
vg1217928334	G -> A	LOC_Os12g29990.2	intron_variant ; MODIFIER	silent_mutation	Average:38.989; most accessible tissue: Minghui63 root, score: 59.105	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1217928334	9.33E-07	NA	mr1858	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
vg1217928334	9.45E-07	NA	mr1859	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