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Detailed information for vg0812679480:

Variant ID: vg0812679480 (JBrowse)	Variation Type: SNP
Chromosome: chr08	Position: 12679480
Reference Allele: A	Alternative Allele: T
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.01, others allele: 0.00, population size: 227. )

Flanking Sequence (100 bp) in Reference Genome:

TACAAAGCTTACAAAAGAGAAGAGGAAAGCTGCTAAAGCCATACCCGAACTCTTCCGAAGGTTTCCGGACTCCTGACTCCTATTCTATTTCTATTCCACC[A/T]
GCTAGATACTACTAAACTAAACTTGAGAGAAATGAGAGAGCTATTGCTTGAGGTGTGTGTTGAAATGAAGAGAGTGAAGCCTTTATATAGAGGTGGTTAT

Reverse complement sequence

ATAACCACCTCTATATAAAGGCTTCACTCTCTTCATTTCAACACACACCTCAAGCAATAGCTCTCTCATTTCTCTCAAGTTTAGTTTAGTAGTATCTAGC[T/A]
GGTGGAATAGAAATAGAATAGGAGTCAGGAGTCCGGAAACCTTCGGAAGAGTTCGGGTATGGCTTTAGCAGCTTTCCTCTTCTCTTTTGTAAGCTTTGTA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	91.60%	1.10%	1.61%	5.63%	NA
All Indica	2759	90.60%	1.80%	2.54%	5.00%	NA
All Japonica	1512	92.10%	0.00%	0.20%	7.67%	NA
Aus	269	98.90%	0.00%	0.74%	0.37%	NA
Indica I	595	97.30%	0.70%	1.34%	0.67%	NA
Indica II	465	94.80%	2.20%	1.29%	1.72%	NA
Indica III	913	83.20%	2.00%	3.94%	10.84%	NA
Indica Intermediate	786	91.60%	2.40%	2.54%	3.44%	NA
Temperate Japonica	767	99.10%	0.00%	0.13%	0.78%	NA
Tropical Japonica	504	86.10%	0.00%	0.00%	13.89%	NA
Japonica Intermediate	241	82.60%	0.00%	0.83%	16.60%	NA
VI/Aromatic	96	93.80%	0.00%	0.00%	6.25%	NA
Intermediate	90	91.10%	2.20%	1.11%	5.56%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0812679480	A -> T	LOC_Os08g21230.1	upstream_gene_variant ; 2484.0bp to feature; MODIFIER	silent_mutation	Average:16.641; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0812679480	A -> T	LOC_Os08g21230-LOC_Os08g21240	intergenic_region ; MODIFIER	silent_mutation	Average:16.641; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N
vg0812679480	A -> DEL	N	N	silent_mutation	Average:16.641; most accessible tissue: Zhenshan97 root, score: 22.162	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0812679480	1.24E-08	5.86E-11	mr1238	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
vg0812679480	3.61E-09	1.35E-10	mr1309	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
vg0812679480	5.30E-07	1.70E-10	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
vg0812679480	3.54E-11	3.54E-11	mr1900	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
vg0812679480	NA	9.87E-07	mr1238_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
vg0812679480	NA	1.60E-08	mr1841_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
vg0812679480	NA	3.10E-06	mr1900_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