Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0234502415:

Variant ID: vg0234502415 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 34502415
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

TTCCCATATTCATATTGATGTTAATGAATCTATACATATATATATATCTAGATTCATTAACATCAATATGAATATGAAAAATGCTAGAATGACTTACATT[A/G]
TGAAACGGAGGAAGTAGTTGGCAAGGGAGGTGGATGTGGGGAGGGGTTGAGTTGCTCTATGTGCTCACTGGTTGAAGCTGATTGTTGCGCTCCTATCTAC

Reverse complement sequence

GTAGATAGGAGCGCAACAATCAGCTTCAACCAGTGAGCACATAGAGCAACTCAACCCCTCCCCACATCCACCTCCCTTGCCAACTACTTCCTCCGTTTCA[T/C]
AATGTAAGTCATTCTAGCATTTTTCATATTCATATTGATGTTAATGAATCTAGATATATATATATGTATAGATTCATTAACATCAATATGAATATGGGAA

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	31.10%	3.80%	1.23%	63.90%	NA
All Indica	2759	2.20%	5.00%	1.78%	90.97%	NA
All Japonica	1512	88.00%	0.10%	0.20%	11.77%	NA
Aus	269	11.20%	13.40%	1.49%	73.98%	NA
Indica I	595	3.20%	0.20%	2.18%	94.45%	NA
Indica II	465	0.90%	0.90%	2.58%	95.70%	NA
Indica III	913	1.10%	13.70%	0.33%	84.88%	NA
Indica Intermediate	786	3.60%	1.10%	2.67%	92.62%	NA
Temperate Japonica	767	92.70%	0.00%	0.26%	7.04%	NA
Tropical Japonica	504	79.20%	0.20%	0.00%	20.63%	NA
Japonica Intermediate	241	91.30%	0.00%	0.41%	8.30%	NA
VI/Aromatic	96	7.30%	2.10%	2.08%	88.54%	NA
Intermediate	90	46.70%	0.00%	0.00%	53.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0234502415	A -> G	LOC_Os02g56360.1	missense_variant ; p.Tyr122Cys; MODERATE	nonsynonymous_codon ; Y122C	Average:9.362; most accessible tissue: Zhenshan97 panicle, score: 20.424	unknown	unknown	TOLERATED	0.11
vg0234502415	A -> G	LOC_Os02g56360.3	missense_variant ; p.Tyr122Cys; MODERATE	nonsynonymous_codon ; Y122C	Average:9.362; most accessible tissue: Zhenshan97 panicle, score: 20.424	unknown	unknown	TOLERATED	0.13
vg0234502415	A -> DEL	LOC_Os02g56360.1	N	frameshift_variant	Average:9.362; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N
vg0234502415	A -> DEL	LOC_Os02g56360.3	N	frameshift_variant	Average:9.362; most accessible tissue: Zhenshan97 panicle, score: 20.424	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0234502415	NA	3.34E-12	mr1322	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
vg0234502415	NA	2.09E-06	mr1322	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
vg0234502415	NA	2.12E-11	mr1325	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
vg0234502415	NA	9.87E-14	mr1326	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
vg0234502415	NA	1.85E-07	mr1338	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
vg0234502415	6.51E-06	6.51E-06	mr1338	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
vg0234502415	NA	1.42E-07	mr1002_2	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