Search for Variation information by Variation ID:

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

Detailed information for vg0214178414:

Variant ID: vg0214178414 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 14178414
Reference Allele: T	Alternative Allele: C
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.50, T: 0.50, others allele: 0.00, population size: 86. )

Flanking Sequence (100 bp) in Reference Genome:

GCATGTTTGGAGATTCCACACGCCGGGGGGCTGCGGACCAGTGCCGCCTTTGCGTGCCTAACGCGGCCCGACTGCTCCTAGGGCAAGCACGACCTGGATG[T/C]
GACGCCGCACGTCGGGCGCTTCGGTCTTCACCCGGCCAACACAGCCCGACTACGCTGCTTCCGCCGCGGGCTCGGGAGTTTCGCCTTTGTGCGCCGCCGC

Reverse complement sequence

GCGGCGGCGCACAAAGGCGAAACTCCCGAGCCCGCGGCGGAAGCAGCGTAGTCGGGCTGTGTTGGCCGGGTGAAGACCGAAGCGCCCGACGTGCGGCGTC[A/G]
CATCCAGGTCGTGCTTGCCCTAGGAGCAGTCGGGCCGCGTTAGGCACGCAAAGGCGGCACTGGTCCGCAGCCCCCCGGCGTGTGGAATCTCCAAACATGC

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	36.50%	3.10%	2.26%	58.13%	NA
All Indica	2759	3.90%	2.10%	2.97%	90.97%	NA
All Japonica	1512	98.40%	0.10%	0.07%	1.46%	NA
Aus	269	1.90%	24.90%	6.69%	66.54%	NA
Indica I	595	4.90%	0.00%	2.86%	92.27%	NA
Indica II	465	4.70%	1.50%	2.80%	90.97%	NA
Indica III	913	1.90%	2.20%	3.29%	92.66%	NA
Indica Intermediate	786	5.10%	4.10%	2.80%	88.04%	NA
Temperate Japonica	767	99.10%	0.00%	0.00%	0.91%	NA
Tropical Japonica	504	97.80%	0.00%	0.20%	1.98%	NA
Japonica Intermediate	241	97.50%	0.40%	0.00%	2.07%	NA
VI/Aromatic	96	76.00%	19.80%	2.08%	2.08%	NA
Intermediate	90	57.80%	0.00%	4.44%	37.78%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0214178414	T -> DEL	N	N	silent_mutation	Average:33.181; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0214178414	T -> C	LOC_Os02g24460.1	upstream_gene_variant ; 4255.0bp to feature; MODIFIER	silent_mutation	Average:33.181; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0214178414	T -> C	LOC_Os02g24480.1	upstream_gene_variant ; 159.0bp to feature; MODIFIER	silent_mutation	Average:33.181; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0214178414	T -> C	LOC_Os02g24470.1	downstream_gene_variant ; 1826.0bp to feature; MODIFIER	silent_mutation	Average:33.181; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N
vg0214178414	T -> C	LOC_Os02g24470-LOC_Os02g24480	intergenic_region ; MODIFIER	silent_mutation	Average:33.181; most accessible tissue: Zhenshan97 panicle, score: 49.416	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0214178414	NA	1.44E-09	mr1338_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
vg0214178414	NA	6.53E-06	mr1992_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