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Detailed information for vg0812016141:

Variant ID: vg0812016141 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12016141
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.97, G: 0.03, others allele: 0.00, population size: 113. )

Flanking Sequence (100 bp) in Reference Genome:

AGCCATGCCCCTTCCATGATCATGCCAAGAGAACAAAATGGAGAGAAAGTATAGGAAAAAAGGAGAATAAATTTTTCCATCATTCCACAATATATTTTAC[G/T]
TTTTCATTTTCCACCACAAATAAAAACCCTTGATCTAAGAGCATGATTGATGATCTTCTTGAGTCCACATTTTTGGTTTTGCAATATATATGATGCAGGT

Reverse complement sequence

ACCTGCATCATATATATTGCAAAACCAAAAATGTGGACTCAAGAAGATCATCAATCATGCTCTTAGATCAAGGGTTTTTATTTGTGGTGGAAAATGAAAA[C/A]
GTAAAATATATTGTGGAATGATGGAAAAATTTATTCTCCTTTTTTCCTATACTTTCTCTCCATTTTGTTCTCTTGGCATGATCATGGAAGGGGCATGGCT

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	24.20%	19.60%	1.12%	55.16%	NA
All Indica	2759	12.00%	10.80%	0.54%	76.66%	NA
All Japonica	1512	51.50%	33.50%	2.38%	12.57%	NA
Aus	269	1.90%	1.10%	0.00%	97.03%	NA
Indica I	595	30.60%	2.50%	1.01%	65.88%	NA
Indica II	465	9.50%	8.80%	0.65%	81.08%	NA
Indica III	913	1.00%	17.60%	0.11%	81.27%	NA
Indica Intermediate	786	12.30%	10.20%	0.64%	76.84%	NA
Temperate Japonica	767	85.50%	10.20%	0.00%	4.30%	NA
Tropical Japonica	504	9.90%	59.70%	7.14%	23.21%	NA
Japonica Intermediate	241	30.30%	53.10%	0.00%	16.60%	NA
VI/Aromatic	96	0.00%	90.60%	0.00%	9.38%	NA
Intermediate	90	28.90%	33.30%	2.22%	35.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812016141	G -> T	LOC_Os08g20050.1	downstream_gene_variant ; 1059.0bp to feature; MODIFIER	silent_mutation	Average:12.811; most accessible tissue: Callus, score: 25.742	N	N	N	N
vg0812016141	G -> T	LOC_Os08g20050-LOC_Os08g20060	intergenic_region ; MODIFIER	silent_mutation	Average:12.811; most accessible tissue: Callus, score: 25.742	N	N	N	N
vg0812016141	G -> DEL	N	N	silent_mutation	Average:12.811; most accessible tissue: Callus, score: 25.742	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812016141	NA	6.06E-07	mr1045	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
vg0812016141	NA	1.39E-06	mr1309	Ind_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
vg0812016141	NA	1.75E-07	mr1521	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
vg0812016141	NA	2.14E-06	mr1668	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
vg0812016141	NA	3.13E-07	mr1841	Ind_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
vg0812016141	NA	1.08E-07	mr1864	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
vg0812016141	9.56E-08	9.55E-08	mr1900	Ind_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
vg0812016141	NA	2.61E-06	mr1194_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
vg0812016141	NA	9.99E-06	mr1362_2	Ind_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
vg0812016141	NA	7.41E-07	mr1404_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
vg0812016141	NA	4.26E-08	mr1521_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
vg0812016141	NA	1.17E-08	mr1671_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
vg0812016141	NA	1.19E-08	mr1746_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
vg0812016141	NA	6.78E-08	mr1794_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
vg0812016141	2.47E-06	4.27E-07	mr1836_2	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