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Detailed information for vg1222071730:

Variant ID: vg1222071730 (JBrowse)	Variation Type: SNP
Chromosome: chr12	Position: 22071730
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: 222. )

Flanking Sequence (100 bp) in Reference Genome:

CTGAACTAGTGTTATGCGTAATGATCATGTTTCTCTTTCCATCCCTCTCTTTGTTCCATGTCATCAAATTTATTTGCACGATAATAGCGAGAGCCCACTA[G/A]
TAAAGACCATCGTACATACCCTAACGCAACCAGCTCTTTCCATGGGCTCTTAGCAAGTGAGCACAAAGTTCCGAGGAAAGCCAATGGAAGTTAAAAGATT

Reverse complement sequence

AATCTTTTAACTTCCATTGGCTTTCCTCGGAACTTTGTGCTCACTTGCTAAGAGCCCATGGAAAGAGCTGGTTGCGTTAGGGTATGTACGATGGTCTTTA[C/T]
TAGTGGGCTCTCGCTATTATCGTGCAAATAAATTTGATGACATGGAACAAAGAGAGGGATGGAAAGAGAAACATGATCATTACGCATAACACTAGTTCAG

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	81.50%	9.60%	0.78%	8.04%	NA
All Indica	2759	82.20%	7.90%	1.27%	8.66%	NA
All Japonica	1512	90.70%	2.30%	0.07%	6.94%	NA
Aus	269	15.60%	71.00%	0.37%	13.01%	NA
Indica I	595	97.10%	0.20%	1.85%	0.84%	NA
Indica II	465	91.40%	8.20%	0.00%	0.43%	NA
Indica III	913	66.00%	14.00%	1.86%	18.07%	NA
Indica Intermediate	786	84.20%	6.40%	0.89%	8.52%	NA
Temperate Japonica	767	96.50%	1.30%	0.00%	2.22%	NA
Tropical Japonica	504	78.80%	4.60%	0.20%	16.47%	NA
Japonica Intermediate	241	97.10%	0.80%	0.00%	2.07%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	91.10%	7.80%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1222071730	G -> DEL	N	N	silent_mutation	Average:42.908; most accessible tissue: Callus, score: 78.696	N	N	N	N
vg1222071730	G -> A	LOC_Os12g36030-LOC_Os12g36040	intergenic_region ; MODIFIER	silent_mutation	Average:42.908; most accessible tissue: Callus, score: 78.696	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1222071730	4.80E-06	NA	mr1789	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