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Detailed information for vg0517004979:

Variant ID: vg0517004979 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 17004979
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.93, T: 0.07, others allele: 0.00, population size: 232. )

Flanking Sequence (100 bp) in Reference Genome:

CCTACCGATGTAAGGGCACTGTAAAATGGAATCACAATATAATACTAGGTCTTTCAGTTCGTTTGATAAAGAAATATGTTATTAGTGAGTTAGGGACACA[T/C]
TCAGACAACGACCAGCAACGAGCTAGTATATAACTACAAGCCTACACAAGTGACTAGCTCTACATATATGTGGTGCACCTATCTCAGAAAGCCTAAGCTA

Reverse complement sequence

TAGCTTAGGCTTTCTGAGATAGGTGCACCACATATATGTAGAGCTAGTCACTTGTGTAGGCTTGTAGTTATATACTAGCTCGTTGCTGGTCGTTGTCTGA[A/G]
TGTGTCCCTAACTCACTAATAACATATTTCTTTATCAAACGAACTGAAAGACCTAGTATTATATTGTGATTCCATTTTACAGTGCCCTTACATCGGTAGG

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	72.60%	27.30%	0.13%	0.04%	NA
All Indica	2759	61.70%	38.10%	0.18%	0.07%	NA
All Japonica	1512	97.40%	2.60%	0.00%	0.00%	NA
Aus	269	32.00%	68.00%	0.00%	0.00%	NA
Indica I	595	46.70%	53.10%	0.17%	0.00%	NA
Indica II	465	67.50%	31.80%	0.43%	0.22%	NA
Indica III	913	71.60%	28.30%	0.11%	0.00%	NA
Indica Intermediate	786	58.00%	41.70%	0.13%	0.13%	NA
Temperate Japonica	767	95.40%	4.60%	0.00%	0.00%	NA
Tropical Japonica	504	99.80%	0.20%	0.00%	0.00%	NA
Japonica Intermediate	241	98.80%	1.20%	0.00%	0.00%	NA
VI/Aromatic	96	96.90%	3.10%	0.00%	0.00%	NA
Intermediate	90	84.40%	14.40%	1.11%	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
vg0517004979	T -> DEL	N	N	silent_mutation	Average:70.727; most accessible tissue: Callus, score: 86.665	N	N	N	N
vg0517004979	T -> C	LOC_Os05g29010.2	downstream_gene_variant ; 1517.0bp to feature; MODIFIER	silent_mutation	Average:70.727; most accessible tissue: Callus, score: 86.665	N	N	N	N
vg0517004979	T -> C	LOC_Os05g29010.1	downstream_gene_variant ; 1517.0bp to feature; MODIFIER	silent_mutation	Average:70.727; most accessible tissue: Callus, score: 86.665	N	N	N	N
vg0517004979	T -> C	LOC_Os05g29000-LOC_Os05g29010	intergenic_region ; MODIFIER	silent_mutation	Average:70.727; most accessible tissue: Callus, score: 86.665	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0517004979	4.50E-06	4.50E-06	mr1014	Jap_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
vg0517004979	NA	9.79E-06	mr1044	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