Search for Variation information by Variation ID:

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

Detailed information for vg0401231092:

Variant ID: vg0401231092 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1231092
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele : T (evidence from allele frequency in Oryza rufipogon: T: 0.77, C: 0.23, others allele: 0.00, population size: 213. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCCCCCATAGACTATCCATTTTATAAAAGCCCGTTGCATACATTGGCACACTTGACGGGCAAGAGTTAATCAATATCTCCCTTTCCCCATAAGTTAGA[C/T]
GTCCACTCTTGCAAGTGCCTAACCTTTTCTCCCCTTTTCTAGGCCACCTGCTGAAGATTTTTCCTCCCAATTTTATGTCAGGAGTTGTAGGTAAGCGGTA

Reverse complement sequence

TACCGCTTACCTACAACTCCTGACATAAAATTGGGAGGAAAAATCTTCAGCAGGTGGCCTAGAAAAGGGGAGAAAAGGTTAGGCACTTGCAAGAGTGGAC[G/A]
TCTAACTTATGGGGAAAGGGAGATATTGATTAACTCTTGCCCGTCAAGTGTGCCAATGTATGCAACGGGCTTTTATAAAATGGATAGTCTATGGGGGAGA

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	49.80%	49.70%	0.38%	0.11%	NA
All Indica	2759	51.70%	47.60%	0.47%	0.18%	NA
All Japonica	1512	39.40%	60.60%	0.00%	0.00%	NA
Aus	269	94.80%	5.20%	0.00%	0.00%	NA
Indica I	595	32.10%	66.70%	0.84%	0.34%	NA
Indica II	465	62.80%	36.30%	0.43%	0.43%	NA
Indica III	913	48.80%	51.00%	0.11%	0.00%	NA
Indica Intermediate	786	63.40%	35.90%	0.64%	0.13%	NA
Temperate Japonica	767	45.40%	54.60%	0.00%	0.00%	NA
Tropical Japonica	504	33.90%	66.10%	0.00%	0.00%	NA
Japonica Intermediate	241	31.50%	68.50%	0.00%	0.00%	NA
VI/Aromatic	96	22.90%	75.00%	2.08%	0.00%	NA
Intermediate	90	60.00%	36.70%	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
vg0401231092	C -> DEL	N	N	silent_mutation	Average:43.832; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg0401231092	C -> T	LOC_Os04g03010.1	downstream_gene_variant ; 3484.0bp to feature; MODIFIER	silent_mutation	Average:43.832; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N
vg0401231092	C -> T	LOC_Os04g03020.1	intron_variant ; MODIFIER	silent_mutation	Average:43.832; most accessible tissue: Zhenshan97 young leaf, score: 60.8	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401231092	NA	9.56E-08	mr1036	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
vg0401231092	NA	9.74E-06	mr1036	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
vg0401231092	NA	7.88E-07	mr1861	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