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Detailed information for vg0816784758:

Variant ID: vg0816784758 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 16784758
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: 0.01, others allele: 0.00, population size: 107. )

Flanking Sequence (100 bp) in Reference Genome:

CGCCTTCTCTCGGTGTAGGACGTCGAAGGCAGAGGTTCCGGAGACCTGCTCTCCCGATCGCCGGTGCACGCCGGCGAGTGGGATAGAGTAGTCTACGAGC[G/A]
ACGGCGCAGCACAGAGTAGGAGGCAAACCCTAGATTGATTTCGCATATGTTCATCAAGACGATAAGTCGCGCTGCGCAAGGCTGAGGAGCCAATTTTGCG

Reverse complement sequence

CGCAAAATTGGCTCCTCAGCCTTGCGCAGCGCGACTTATCGTCTTGATGAACATATGCGAAATCAATCTAGGGTTTGCCTCCTACTCTGTGCTGCGCCGT[C/T]
GCTCGTAGACTACTCTATCCCACTCGCCGGCGTGCACCGGCGATCGGGAGAGCAGGTCTCCGGAACCTCTGCCTTCGACGTCCTACACCGAGAGAAGGCG

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	63.40%	10.90%	0.93%	24.80%	NA
All Indica	2759	43.50%	13.50%	1.56%	41.43%	NA
All Japonica	1512	98.90%	0.10%	0.07%	0.93%	NA
Aus	269	47.20%	50.90%	0.00%	1.86%	NA
Indica I	595	58.80%	29.20%	0.50%	11.43%	NA
Indica II	465	40.40%	4.70%	2.15%	52.69%	NA
Indica III	913	29.50%	9.10%	1.86%	59.58%	NA
Indica Intermediate	786	50.10%	11.80%	1.65%	36.39%	NA
Temperate Japonica	767	99.20%	0.10%	0.00%	0.65%	NA
Tropical Japonica	504	98.40%	0.00%	0.00%	1.59%	NA
Japonica Intermediate	241	99.20%	0.00%	0.41%	0.41%	NA
VI/Aromatic	96	96.90%	2.10%	0.00%	1.04%	NA
Intermediate	90	85.60%	4.40%	0.00%	10.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0816784758	G -> A	LOC_Os08g27500.1	missense_variant ; p.Ser51Leu; MODERATE	nonsynonymous_codon ; S51L	Average:32.073; most accessible tissue: Zhenshan97 flag leaf, score: 79.006	unknown	unknown	DELETERIOUS	0.03
vg0816784758	G -> DEL	LOC_Os08g27500.1	N	frameshift_variant	Average:32.073; most accessible tissue: Zhenshan97 flag leaf, score: 79.006	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0816784758	NA	2.51E-08	mr1857	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
vg0816784758	NA	4.60E-06	mr1528_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