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Detailed information for vg0113133591:

Variant ID: vg0113133591 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13133591
Reference Allele: A	Alternative Allele: T
Primary Allele: T	Secondary Allele: A

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.57, A: 0.43, others allele: 0.00, population size: 49. )

Flanking Sequence (100 bp) in Reference Genome:

GACCAATCTTTTGCAGCTGGGCCACTGGGATGGCCGGGGGGAGATGCTTGACTCTATCATCTTTACTGGGCTTGAAACTTGTCACCATTGGCTTCACTTT[A/T]
GTTTTCTTCTTGGGTGTGTCTGTATGTATCTCCAGCTTCTCACCAAGCCCAGTGAAGCGTGGGCTTCTTCTAAGGCCTTCAGTAGAAACTGGGGTTTGAA

Reverse complement sequence

TTCAAACCCCAGTTTCTACTGAAGGCCTTAGAAGAAGCCCACGCTTCACTGGGCTTGGTGAGAAGCTGGAGATACATACAGACACACCCAAGAAGAAAAC[T/A]
AAAGTGAAGCCAATGGTGACAAGTTTCAAGCCCAGTAAAGATGATAGAGTCAAGCATCTCCCCCCGGCCATCCCAGTGGCCCAGCTGCAAAAGATTGGTC

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	63.60%	29.30%	0.04%	6.96%	NA
All Indica	2759	87.50%	2.00%	0.07%	10.44%	NA
All Japonica	1512	12.20%	85.30%	0.00%	2.51%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	89.10%	1.70%	0.00%	9.24%	NA
Indica II	465	86.50%	3.20%	0.00%	10.32%	NA
Indica III	913	86.90%	0.70%	0.00%	12.49%	NA
Indica Intermediate	786	87.70%	3.10%	0.25%	9.03%	NA
Temperate Japonica	767	1.40%	97.10%	0.00%	1.43%	NA
Tropical Japonica	504	31.70%	63.50%	0.00%	4.76%	NA
Japonica Intermediate	241	5.40%	93.40%	0.00%	1.24%	NA
VI/Aromatic	96	94.80%	5.20%	0.00%	0.00%	NA
Intermediate	90	55.60%	41.10%	0.00%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113133591	A -> T	LOC_Os01g23360.1	synonymous_variant ; p.Thr527Thr; LOW	synonymous_codon	Average:46.465; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N
vg0113133591	A -> DEL	LOC_Os01g23360.1	N	frameshift_variant	Average:46.465; most accessible tissue: Zhenshan97 young leaf, score: 69.263	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113133591	NA	6.15E-75	mr1018	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
vg0113133591	1.93E-06	2.78E-64	mr1019	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
vg0113133591	NA	2.08E-06	mr1083	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
vg0113133591	NA	3.13E-69	mr1489	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
vg0113133591	NA	2.79E-82	mr1778	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
vg0113133591	NA	1.02E-75	mr1019_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
vg0113133591	NA	1.95E-06	mr1082_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
vg0113133591	NA	8.52E-78	mr1132_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
vg0113133591	NA	3.76E-07	mr1227_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
vg0113133591	NA	3.39E-58	mr1261_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
vg0113133591	NA	2.18E-17	mr1682_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
vg0113133591	NA	1.13E-16	mr1730_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
vg0113133591	NA	9.71E-76	mr1778_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