Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923).

Detailed information for vg0129717613:

Variant ID: vg0129717613 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 29717613
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 38. )

Flanking Sequence (100 bp) in Reference Genome:

TGAAACGTTGGCACTTTATTTTACATGATATTCAGTCCTTTTAATCACTTTTCTTAACTAAAATACATGTGTTTTGCCCTAAAGTGACCGTATTGCCCTT[C/T]
TGCCTTCTGCATACTTGATCGATCGTATCTTTTCATCTCGTCCGAGTCTACCGTCGTCGTTCCTCCTTTCCTCCCTATGCCGCCGTTCCTCCTTCCCTCC

Reverse complement sequence

GGAGGGAAGGAGGAACGGCGGCATAGGGAGGAAAGGAGGAACGACGACGGTAGACTCGGACGAGATGAAAAGATACGATCGATCAAGTATGCAGAAGGCA[G/A]
AAGGGCAATACGGTCACTTTAGGGCAAAACACATGTATTTTAGTTAAGAAAAGTGATTAAAAGGACTGAATATCATGTAAAATAAAGTGCCAACGTTTCA

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	47.60%	7.00%	1.80%	43.55%	NA
All Indica	2759	35.30%	11.00%	2.39%	51.32%	NA
All Japonica	1512	78.80%	0.10%	0.07%	21.03%	NA
Aus	269	11.20%	7.80%	5.58%	75.46%	NA
Indica I	595	33.60%	16.10%	3.03%	47.23%	NA
Indica II	465	41.10%	5.80%	1.72%	51.40%	NA
Indica III	913	34.20%	9.50%	2.30%	54.00%	NA
Indica Intermediate	786	34.50%	11.80%	2.42%	51.27%	NA
Temperate Japonica	767	99.60%	0.00%	0.00%	0.39%	NA
Tropical Japonica	504	41.50%	0.20%	0.20%	58.13%	NA
Japonica Intermediate	241	90.50%	0.40%	0.00%	9.13%	NA
VI/Aromatic	96	6.20%	1.00%	3.12%	89.58%	NA
Intermediate	90	54.40%	6.70%	0.00%	38.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0129717613	C -> T	LOC_Os01g51680.1	upstream_gene_variant ; 166.0bp to feature; MODIFIER	silent_mutation	Average:19.302; most accessible tissue: Callus, score: 41.098	N	N	N	N
vg0129717613	C -> T	LOC_Os01g51690.1	downstream_gene_variant ; 3310.0bp to feature; MODIFIER	silent_mutation	Average:19.302; most accessible tissue: Callus, score: 41.098	N	N	N	N
vg0129717613	C -> T	LOC_Os01g51670-LOC_Os01g51680	intergenic_region ; MODIFIER	silent_mutation	Average:19.302; most accessible tissue: Callus, score: 41.098	N	N	N	N
vg0129717613	C -> DEL	N	N	silent_mutation	Average:19.302; most accessible tissue: Callus, score: 41.098	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0129717613	3.64E-06	NA	mr1722_2	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
vg0129717613	1.24E-06	NA	mr1722_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