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Detailed information for vg1005051336:

Variant ID: vg1005051336 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 5051336
Reference Allele: G	Alternative Allele: A,T
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: 58. )

Flanking Sequence (100 bp) in Reference Genome:

CTTTTGCTGCTTCAAAAGGTTTTAATTTGTATCAAATGGATGTGAAAAGTGTTTTTCTAAATGGTTTTATACAGGAGGAAGTTTATGTCAAACAACCACC[G/A,T]
GGTTTTGAAAATCCTGATTTTCCCAACCATGTTTTTAAATTGTCTAAAGCTTTGTATGGTTTGAAACTAGCTCCTAGGGCATGGTATGATAGGCTTAAGA

Reverse complement sequence

TCTTAAGCCTATCATACCATGCCCTAGGAGCTAGTTTCAAACCATACAAAGCTTTAGACAATTTAAAAACATGGTTGGGAAAATCAGGATTTTCAAAACC[C/T,A]
GGTGGTTGTTTGACATAAACTTCCTCCTGTATAAAACCATTTAGAAAAACACTTTTCACATCCATTTGATACAAATTAAAACCTTTTGAAGCAGCAAAAG

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	33.60%	0.70%	52.22%	13.44%	T: 0.02%
All Indica	2759	16.90%	1.00%	74.95%	7.21%	NA
All Japonica	1512	66.90%	0.00%	5.95%	27.05%	T: 0.07%
Aus	269	11.50%	1.90%	79.55%	7.06%	NA
Indica I	595	35.30%	2.40%	55.63%	6.72%	NA
Indica II	465	13.50%	0.60%	75.70%	10.11%	NA
Indica III	913	5.40%	0.00%	91.35%	3.29%	NA
Indica Intermediate	786	18.20%	1.30%	70.10%	10.43%	NA
Temperate Japonica	767	78.90%	0.00%	6.00%	15.12%	NA
Tropical Japonica	504	54.20%	0.00%	4.17%	41.47%	T: 0.20%
Japonica Intermediate	241	55.60%	0.00%	9.54%	34.85%	NA
VI/Aromatic	96	41.70%	0.00%	56.25%	2.08%	NA
Intermediate	90	46.70%	0.00%	46.67%	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
vg1005051336	G -> T	LOC_Os10g09350.1	synonymous_variant ; p.Pro1167Pro; LOW	synonymous_codon	Average:5.704; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1005051336	G -> A	LOC_Os10g09350.1	synonymous_variant ; p.Pro1167Pro; LOW	synonymous_codon	Average:5.704; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N
vg1005051336	G -> DEL	LOC_Os10g09350.1	N	frameshift_variant	Average:5.704; most accessible tissue: Zhenshan97 root, score: 10.511	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1005051336	4.18E-06	4.18E-06	mr1591	Jap_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