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Detailed information for vg0314128282:

Variant ID: vg0314128282 (JBrowse)	Variation Type: SNP
Chromosome: chr03	Position: 14128282
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.60, A: 0.40, others allele: 0.00, population size: 63. )

Flanking Sequence (100 bp) in Reference Genome:

TACCAACAAGCCCTTCGCCGCTACCACGAGAAGCGCATTCGAGCACGCATACTTTCGATCGGCGACTACGTCCTCCAAAGGGTTCAAAGCCAAGCAGGGC[G/A]
AAACAAGCTCTCACCCAAATAGGAAGGACCATACACGATCACACAAGTCTTGCGACCAGGCGCATTCAAAATTGCAGACAGCGATGGCCACGAGTTGGCA

Reverse complement sequence

TGCCAACTCGTGGCCATCGCTGTCTGCAATTTTGAATGCGCCTGGTCGCAAGACTTGTGTGATCGTGTATGGTCCTTCCTATTTGGGTGAGAGCTTGTTT[C/T]
GCCCTGCTTGGCTTTGAACCCTTTGGAGGACGTAGTCGCCGATCGAAAGTATGCGTGCTCGAATGCGCTTCTCGTGGTAGCGGCGAAGGGCTTGTTGGTA

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	84.30%	2.90%	3.70%	9.06%	NA
All Indica	2759	77.00%	4.80%	5.87%	12.36%	NA
All Japonica	1512	94.60%	0.00%	0.07%	5.29%	NA
Aus	269	96.30%	0.70%	2.60%	0.37%	NA
Indica I	595	74.60%	2.20%	9.08%	14.12%	NA
Indica II	465	72.30%	2.40%	4.95%	20.43%	NA
Indica III	913	80.00%	8.00%	4.71%	7.34%	NA
Indica Intermediate	786	78.10%	4.50%	5.34%	12.09%	NA
Temperate Japonica	767	91.70%	0.00%	0.13%	8.21%	NA
Tropical Japonica	504	97.60%	0.00%	0.00%	2.38%	NA
Japonica Intermediate	241	97.90%	0.00%	0.00%	2.07%	NA
VI/Aromatic	96	96.90%	1.00%	2.08%	0.00%	NA
Intermediate	90	87.80%	2.20%	3.33%	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
vg0314128282	G -> A	LOC_Os03g24790.1	missense_variant ; p.Arg516Gln; MODERATE	nonsynonymous_codon ; R516Q	Average:12.806; most accessible tissue: Minghui63 young leaf, score: 24.836	unknown	unknown	TOLERATED	0.21
vg0314128282	G -> DEL	LOC_Os03g24790.1	N	frameshift_variant	Average:12.806; most accessible tissue: Minghui63 young leaf, score: 24.836	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0314128282	7.38E-06	7.38E-06	mr1239	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