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Detailed information for vg0522015078:

Variant ID: vg0522015078 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 22015078
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.88, C: 0.12, others allele: 0.00, population size: 103. )

Flanking Sequence (100 bp) in Reference Genome:

TTAAGCTTGAATCAACAATCAAAATTCATGATTTCATACGATTTATAATGCAACATCTTAACAAGCACATAGGTTGAAAAATTAACACTAAACACATATA[C/T]
CTATTGTATTTATCACTCTTTCTCAAATAACCTTTAGCACAAAACAACAAAGAGAGTTTTTTTAATTTTTTCTTGTTCTTGAGCCTTTTTGCTCATATTT

Reverse complement sequence

AAATATGAGCAAAAAGGCTCAAGAACAAGAAAAAATTAAAAAAACTCTCTTTGTTGTTTTGTGCTAAAGGTTATTTGAGAAAGAGTGATAAATACAATAG[G/A]
TATATGTGTTTAGTGTTAATTTTTCAACCTATGTGCTTGTTAAGATGTTGCATTATAAATCGTATGAAATCATGAATTTTGATTGTTGATTCAAGCTTAA

Allele Frequencies:

Populations	Population Size	Frequency of T(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	61.60%	38.20%	0.23%	0.00%	NA
All Indica	2759	97.80%	2.00%	0.25%	0.00%	NA
All Japonica	1512	1.50%	98.50%	0.00%	0.00%	NA
Aus	269	54.30%	45.40%	0.37%	0.00%	NA
Indica I	595	99.00%	0.80%	0.17%	0.00%	NA
Indica II	465	97.60%	1.90%	0.43%	0.00%	NA
Indica III	913	99.20%	0.70%	0.11%	0.00%	NA
Indica Intermediate	786	95.20%	4.50%	0.38%	0.00%	NA
Temperate Japonica	767	1.30%	98.70%	0.00%	0.00%	NA
Tropical Japonica	504	1.00%	99.00%	0.00%	0.00%	NA
Japonica Intermediate	241	2.90%	97.10%	0.00%	0.00%	NA
VI/Aromatic	96	2.10%	97.90%	0.00%	0.00%	NA
Intermediate	90	50.00%	46.70%	3.33%	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
vg0522015078	C -> T	LOC_Os05g37610.1	downstream_gene_variant ; 1978.0bp to feature; MODIFIER	silent_mutation	Average:13.613; most accessible tissue: Zhenshan97 flower, score: 19.041	N	N	N	N
vg0522015078	C -> T	LOC_Os05g37620.1	downstream_gene_variant ; 931.0bp to feature; MODIFIER	silent_mutation	Average:13.613; most accessible tissue: Zhenshan97 flower, score: 19.041	N	N	N	N
vg0522015078	C -> T	LOC_Os05g37610-LOC_Os05g37620	intergenic_region ; MODIFIER	silent_mutation	Average:13.613; most accessible tissue: Zhenshan97 flower, score: 19.041	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0522015078	NA	1.01E-48	mr1125	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
vg0522015078	NA	8.43E-58	mr1594	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
vg0522015078	NA	2.45E-30	mr1737	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
vg0522015078	NA	4.64E-36	mr1037_2	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