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Detailed information for vg0115159369:

Variant ID: vg0115159369 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 15159369
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.95, T: 0.04, others allele: 0.00, population size: 111. )

Flanking Sequence (100 bp) in Reference Genome:

GCATATAAGGGGCAGATGACTCGGTATGGCGAGCTGTGGCGCTCGCCATACCTTGATCTGCTAGTGAGACCCCCCCGGGGCGCGTCCTCCTTCCTAGGAC[G/T]
CCGCGCCGCACCGGCACGATCGAGAGAGGGAGAGTGAGAACATGGCGCGATCGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATGGGCCTAATTAGTTGG

Reverse complement sequence

CCAACTAATTAGGCCCATTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGATCGCGCCATGTTCTCACTCTCCCTCTCTCGATCGTGCCGGTGCGGCGCGG[C/A]
GTCCTAGGAAGGAGGACGCGCCCCGGGGGGGTCTCACTAGCAGATCAAGGTATGGCGAGCGCCACAGCTCGCCATACCGAGTCATCTGCCCCTTATATGC

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	78.10%	21.90%	0.04%	0.00%	NA
All Indica	2759	65.00%	34.90%	0.07%	0.00%	NA
All Japonica	1512	100.00%	0.00%	0.00%	0.00%	NA
Aus	269	81.80%	18.20%	0.00%	0.00%	NA
Indica I	595	94.10%	5.90%	0.00%	0.00%	NA
Indica II	465	54.40%	45.60%	0.00%	0.00%	NA
Indica III	913	54.10%	45.90%	0.00%	0.00%	NA
Indica Intermediate	786	61.80%	37.90%	0.25%	0.00%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	100.00%	0.00%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	78.90%	21.10%	0.00%	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
vg0115159369	G -> T	LOC_Os01g27170.1	upstream_gene_variant ; 2124.0bp to feature; MODIFIER	silent_mutation	Average:59.67; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N
vg0115159369	G -> T	LOC_Os01g27180.1	upstream_gene_variant ; 484.0bp to feature; MODIFIER	silent_mutation	Average:59.67; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N
vg0115159369	G -> T	LOC_Os01g27190.1	upstream_gene_variant ; 1054.0bp to feature; MODIFIER	silent_mutation	Average:59.67; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N
vg0115159369	G -> T	LOC_Os01g27180-LOC_Os01g27190	intergenic_region ; MODIFIER	silent_mutation	Average:59.67; most accessible tissue: Zhenshan97 young leaf, score: 75.039	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0115159369	NA	3.01E-06	mr1550	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
vg0115159369	NA	2.80E-10	mr1565	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
vg0115159369	NA	1.77E-08	mr1565	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
vg0115159369	8.45E-06	8.45E-06	mr1762	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
vg0115159369	1.88E-06	1.29E-06	mr1948	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
vg0115159369	NA	2.41E-06	mr1402_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
vg0115159369	NA	3.13E-06	mr1795_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