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Detailed information for vg0114877604:

Variant ID: vg0114877604 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 14877604
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.90, A: 0.10, others allele: 0.00, population size: 77. )

Flanking Sequence (100 bp) in Reference Genome:

GGGGGGTTACGAACCGGAATTACAAACGATTTCTCCACCAGTGGGAGGTAGTATGTTTGTAAGTAAACATGCAGTTAGAGTTACCTTGGTCGCAGTCACC[G/A]
TCGAGGTAGGGATTGCTATTAGTATATTTGATGCATGCACAACGGTAGCCTCCATTTTCGTCATCCGCATCCAAACATTTGTTATCACCACAAGCATACC

Reverse complement sequence

GGTATGCTTGTGGTGATAACAAATGTTTGGATGCGGATGACGAAAATGGAGGCTACCGTTGTGCATGCATCAAATATACTAATAGCAATCCCTACCTCGA[C/T]
GGTGACTGCGACCAAGGTAACTCTAACTGCATGTTTACTTACAAACATACTACCTCCCACTGGTGGAGAAATCGTTTGTAATTCCGGTTCGTAACCCCCC

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	69.20%	15.50%	0.85%	14.47%	NA
All Indica	2759	56.60%	25.90%	1.23%	16.24%	NA
All Japonica	1512	87.50%	0.20%	0.07%	12.24%	NA
Aus	269	81.40%	0.70%	1.86%	15.99%	NA
Indica I	595	32.40%	50.80%	0.84%	15.97%	NA
Indica II	465	57.60%	31.00%	0.22%	11.18%	NA
Indica III	913	68.10%	6.80%	1.75%	23.33%	NA
Indica Intermediate	786	60.90%	26.30%	1.53%	11.20%	NA
Temperate Japonica	767	94.70%	0.00%	0.00%	5.35%	NA
Tropical Japonica	504	91.90%	0.20%	0.20%	7.74%	NA
Japonica Intermediate	241	55.60%	0.80%	0.00%	43.57%	NA
VI/Aromatic	96	97.90%	0.00%	0.00%	2.08%	NA
Intermediate	90	81.10%	12.20%	0.00%	6.67%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0114877604	G -> A	LOC_Os01g26240.1	synonymous_variant ; p.Asp302Asp; LOW	synonymous_codon	Average:31.121; most accessible tissue: Callus, score: 57.231	N	N	N	N
vg0114877604	G -> DEL	LOC_Os01g26240.1	N	frameshift_variant	Average:31.121; most accessible tissue: Callus, score: 57.231	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0114877604	9.66E-07	3.70E-08	mr1707_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