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Detailed information for vg0807994964:

Variant ID: vg0807994964 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 7994964
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 354. )

Flanking Sequence (100 bp) in Reference Genome:

AAACACGTCACCCTTACAAACCACCTTAGAGAAGAGCTTGTTTGGGTTGGACGTGACAAAACCAACATAGAGTGTTCCCTCAAGCACGGTAAGGAGCTCA[G/T]
TAGCACGGGGATGTATGTGTGGTGGGTTCACACCCATTGGCGCGTAGTCGATACGAGCTAGTGAGATGCCAAGGGTATTGAGACCCGGAAACTCCATGAC

Reverse complement sequence

GTCATGGAGTTTCCGGGTCTCAATACCCTTGGCATCTCACTAGCTCGTATCGACTACGCGCCAATGGGTGTGAACCCACCACACATACATCCCCGTGCTA[C/A]
TGAGCTCCTTACCGTGCTTGAGGGAACACTCTATGTTGGTTTTGTCACGTCCAACCCAAACAAGCTCTTCTCTAAGGTGGTTTGTAAGGGTGACGTGTTT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.40%	8.30%	0.30%	0.00%	NA
All Indica	2759	99.80%	0.20%	0.00%	0.00%	NA
All Japonica	1512	74.10%	25.10%	0.86%	0.00%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	100.00%	0.00%	0.00%	0.00%	NA
Indica II	465	99.60%	0.40%	0.00%	0.00%	NA
Indica III	913	99.80%	0.20%	0.00%	0.00%	NA
Indica Intermediate	786	99.70%	0.30%	0.00%	0.00%	NA
Temperate Japonica	767	96.30%	2.70%	0.91%	0.00%	NA
Tropical Japonica	504	33.10%	65.90%	0.99%	0.00%	NA
Japonica Intermediate	241	88.80%	10.80%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	90.00%	8.90%	1.11%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0807994964	G -> T	LOC_Os08g13440.1	missense_variant ; p.Thr119Asn; MODERATE	nonsynonymous_codon ; T119N	Average:59.997; most accessible tissue: Zhenshan97 young leaf, score: 83.831	possibly damaging	1.89	DELETERIOUS	0.00
vg0807994964	G -> T	LOC_Os08g13440.2	missense_variant ; p.Thr117Asn; MODERATE	nonsynonymous_codon ; T117N	Average:59.997; most accessible tissue: Zhenshan97 young leaf, score: 83.831	possibly damaging	1.89	DELETERIOUS	0.00
vg0807994964	G -> T	LOC_Os08g13440.3	missense_variant ; p.Thr95Asn; MODERATE	nonsynonymous_codon ; T95N	Average:59.997; most accessible tissue: Zhenshan97 young leaf, score: 83.831	possibly damaging	1.821	DELETERIOUS	0.00

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0807994964	NA	4.62E-07	mr1077	Jap_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
vg0807994964	4.63E-06	4.63E-06	mr1146	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
vg0807994964	NA	4.72E-07	mr1206	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
vg0807994964	NA	1.27E-06	mr1248	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
vg0807994964	NA	3.00E-08	mr1668	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
vg0807994964	NA	3.06E-07	mr1668_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
vg0807994964	NA	1.96E-08	mr1800_2	Jap_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