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Detailed information for vg0110161014:

Variant ID: vg0110161014 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10161014
Reference Allele: G	Alternative Allele: T
Primary Allele: T	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.92, T: 0.09, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:

TATTTCTGCCATTAAAGATTGGCAATTGAACGAACGAATGTGTATGACCCCACCCACACGTCCATGCCCATGTTGATTTAGATTACATTGTACTTTTGTG[G/T]
TGCTTTGTAGGCATGGTCAGTTGCATACACTGGCCGTTGTAGAGGCTGAATGCATCATCGAAGCTGGGAACGTGGTTGAGGGGCCGATGTGATTATGGTG

Reverse complement sequence

CACCATAATCACATCGGCCCCTCAACCACGTTCCCAGCTTCGATGATGCATTCAGCCTCTACAACGGCCAGTGTATGCAACTGACCATGCCTACAAAGCA[C/A]
CACAAAAGTACAATGTAATCTAAATCAACATGGGCATGGACGTGTGGGTGGGGTCATACACATTCGTTCGTTCAATTGCCAATCTTTAATGGCAGAAATA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	55.80%	43.90%	0.15%	0.11%	NA
All Indica	2759	88.90%	10.80%	0.18%	0.18%	NA
All Japonica	1512	3.00%	97.00%	0.00%	0.00%	NA
Aus	269	5.90%	93.70%	0.37%	0.00%	NA
Indica I	595	97.50%	2.20%	0.00%	0.34%	NA
Indica II	465	85.60%	14.00%	0.43%	0.00%	NA
Indica III	913	87.50%	12.20%	0.22%	0.11%	NA
Indica Intermediate	786	85.90%	13.70%	0.13%	0.25%	NA
Temperate Japonica	767	1.40%	98.60%	0.00%	0.00%	NA
Tropical Japonica	504	5.20%	94.80%	0.00%	0.00%	NA
Japonica Intermediate	241	3.70%	96.30%	0.00%	0.00%	NA
VI/Aromatic	96	83.30%	15.60%	1.04%	0.00%	NA
Intermediate	90	50.00%	50.00%	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
vg0110161014	G -> T	LOC_Os01g18150.1	upstream_gene_variant ; 3388.0bp to feature; MODIFIER	silent_mutation	Average:70.499; most accessible tissue: Zhenshan97 flower, score: 84.964	N	N	N	N
vg0110161014	G -> T	LOC_Os01g18130.1	downstream_gene_variant ; 2332.0bp to feature; MODIFIER	silent_mutation	Average:70.499; most accessible tissue: Zhenshan97 flower, score: 84.964	N	N	N	N
vg0110161014	G -> T	LOC_Os01g18140.1	downstream_gene_variant ; 336.0bp to feature; MODIFIER	silent_mutation	Average:70.499; most accessible tissue: Zhenshan97 flower, score: 84.964	N	N	N	N
vg0110161014	G -> T	LOC_Os01g18140-LOC_Os01g18150	intergenic_region ; MODIFIER	silent_mutation	Average:70.499; most accessible tissue: Zhenshan97 flower, score: 84.964	N	N	N	N
vg0110161014	G -> DEL	N	N	silent_mutation	Average:70.499; most accessible tissue: Zhenshan97 flower, score: 84.964	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110161014	4.14E-07	4.14E-07	mr1151_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