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Detailed information for vg0119055917:

Variant ID: vg0119055917 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 19055917
Reference Allele: T	Alternative Allele: A
Primary Allele: A	Secondary Allele: T

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, T: 0.00, others allele: 0.00, population size: 222. )

Flanking Sequence (100 bp) in Reference Genome:

TAATCTTATGCACCATATAAATATTATCAATCCAGATAATCGACACCTTGTGACTCAAAATTTCTACTATGCATTTACTACGGTGCATGTTAGAAAAAAC[T/A]
TTTTTTTTCTTTTTGCAAATTAATGTGGATTTATTTCAGGCAGGATTCAATATGTGTCCTAACCTACATTTTTTTCTTATTCTTGAATCCCATTCTTAAA

Reverse complement sequence

TTTAAGAATGGGATTCAAGAATAAGAAAAAAATGTAGGTTAGGACACATATTGAATCCTGCCTGAAATAAATCCACATTAATTTGCAAAAAGAAAAAAAA[A/T]
GTTTTTTCTAACATGCACCGTAGTAAATGCATAGTAGAAATTTTGAGTCACAAGGTGTCGATTATCTGGATTGATAATATTTATATGGTGCATAAGATTA

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	62.10%	37.30%	0.55%	0.00%	NA
All Indica	2759	88.90%	10.50%	0.62%	0.00%	NA
All Japonica	1512	20.60%	79.00%	0.46%	0.00%	NA
Aus	269	48.30%	51.70%	0.00%	0.00%	NA
Indica I	595	99.50%	0.50%	0.00%	0.00%	NA
Indica II	465	94.80%	5.20%	0.00%	0.00%	NA
Indica III	913	80.00%	18.30%	1.75%	0.00%	NA
Indica Intermediate	786	87.70%	12.20%	0.13%	0.00%	NA
Temperate Japonica	767	5.20%	94.40%	0.39%	0.00%	NA
Tropical Japonica	504	29.80%	69.80%	0.40%	0.00%	NA
Japonica Intermediate	241	50.20%	49.00%	0.83%	0.00%	NA
VI/Aromatic	96	1.00%	99.00%	0.00%	0.00%	NA
Intermediate	90	45.60%	52.20%	2.22%	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
vg0119055917	T -> A	LOC_Os01g34540.1	upstream_gene_variant ; 1752.0bp to feature; MODIFIER	silent_mutation	Average:40.395; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0119055917	T -> A	LOC_Os01g34550.1	upstream_gene_variant ; 311.0bp to feature; MODIFIER	silent_mutation	Average:40.395; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0119055917	T -> A	LOC_Os01g34560.1	upstream_gene_variant ; 3316.0bp to feature; MODIFIER	silent_mutation	Average:40.395; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N
vg0119055917	T -> A	LOC_Os01g34540-LOC_Os01g34550	intergenic_region ; MODIFIER	silent_mutation	Average:40.395; most accessible tissue: Zhenshan97 young leaf, score: 59.009	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0119055917	NA	1.14E-18	mr1228	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