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Detailed information for vg0215099780:

Variant ID: vg0215099780 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 15099780
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, A: 0.02, others allele: 0.00, population size: 120. )

Flanking Sequence (100 bp) in Reference Genome:

CCGAGTTAAATATGAGGCAGAGAAGATGGTTGGAACTAATCAAGGATTACGATCTTGGAATTCATTACCATCCCGGTAAAGCTAATGTGGTCGCTGATGC[G/A]
CTAAGTCGCAAGACCTACTACAATGTAGCTCAAATATGGCCAGACCAAGATCGCCTGTGCGGAGAATTGGAGAAGTTAAGGCTGACCGTGGTACAGTCAG

Reverse complement sequence

CTGACTGTACCACGGTCAGCCTTAACTTCTCCAATTCTCCGCACAGGCGATCTTGGTCTGGCCATATTTGAGCTACATTGTAGTAGGTCTTGCGACTTAG[C/T]
GCATCAGCGACCACATTAGCTTTACCGGGATGGTAATGAATTCCAAGATCGTAATCCTTGATTAGTTCCAACCATCTTCTCTGCCTCATATTTAACTCGG

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	37.70%	21.30%	23.38%	17.56%	NA
All Indica	2759	5.10%	31.60%	35.12%	28.23%	NA
All Japonica	1512	98.40%	0.20%	0.73%	0.66%	NA
Aus	269	11.20%	47.60%	34.57%	6.69%	NA
Indica I	595	3.20%	41.50%	28.24%	27.06%	NA
Indica II	465	6.00%	20.60%	35.05%	38.28%	NA
Indica III	913	4.20%	31.00%	39.54%	25.30%	NA
Indica Intermediate	786	7.00%	31.20%	35.24%	26.59%	NA
Temperate Japonica	767	99.10%	0.00%	0.39%	0.52%	NA
Tropical Japonica	504	97.60%	0.40%	1.19%	0.79%	NA
Japonica Intermediate	241	97.90%	0.40%	0.83%	0.83%	NA
VI/Aromatic	96	78.10%	2.10%	19.79%	0.00%	NA
Intermediate	90	55.60%	4.40%	14.44%	25.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0215099780	G -> A	LOC_Os02g25770.1	synonymous_variant ; p.Ala1080Ala; LOW	synonymous_codon	Average:11.638; most accessible tissue: Callus, score: 20.395	N	N	N	N
vg0215099780	G -> DEL	LOC_Os02g25770.1	N	frameshift_variant	Average:11.638; most accessible tissue: Callus, score: 20.395	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0215099780	NA	5.97E-06	mr1679_2	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