Search for Variation information by Variation ID:

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

Detailed information for vg0221873638:

Variant ID: vg0221873638 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 21873638
Reference Allele: C	Alternative Allele: T
Primary Allele: T	Secondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACGCGAGGTGGACCCGGCCCACCGGTTCCCCTCCCTCTCTCCCCGCGCGTGCCTTTGGGCCGCCTTCTCGGGCCGGCCGGCCCATTTAGCTCGGCCGAGC[C/T]
GCCCTTTTCTCTCGGGCCGCACCCTAGCCGCCTGAGGGAAGTCTATTTCCCCTCCCTCTTTCTTTTCTTTTTTCAAAAGGGTTTAATTAAATCCTTTTTC

Reverse complement sequence

GAAAAAGGATTTAATTAAACCCTTTTGAAAAAAGAAAAGAAAGAGGGAGGGGAAATAGACTTCCCTCAGGCGGCTAGGGTGCGGCCCGAGAGAAAAGGGC[G/A]
GCTCGGCCGAGCTAAATGGGCCGGCCGGCCCGAGAAGGCGGCCCAAAGGCACGCGCGGGGAGAGAGGGAGGGGAACCGGTGGGCCGGGTCCACCTCGCGT

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	66.10%	33.70%	0.15%	0.00%	NA
All Indica	2759	97.50%	2.40%	0.07%	0.00%	NA
All Japonica	1512	7.90%	92.00%	0.07%	0.00%	NA
Aus	269	98.90%	0.70%	0.37%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	98.90%	1.10%	0.00%	0.00%	NA
Indica III	913	98.10%	1.80%	0.11%	0.00%	NA
Indica Intermediate	786	95.30%	4.60%	0.13%	0.00%	NA
Temperate Japonica	767	1.20%	98.80%	0.00%	0.00%	NA
Tropical Japonica	504	19.40%	80.60%	0.00%	0.00%	NA
Japonica Intermediate	241	5.40%	94.20%	0.41%	0.00%	NA
VI/Aromatic	96	8.30%	90.60%	1.04%	0.00%	NA
Intermediate	90	46.70%	51.10%	2.22%	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
vg0221873638	C -> T	LOC_Os02g36230.1	downstream_gene_variant ; 4058.0bp to feature; MODIFIER	silent_mutation	Average:32.08; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N
vg0221873638	C -> T	LOC_Os02g36230-LOC_Os02g36250	intergenic_region ; MODIFIER	silent_mutation	Average:32.08; most accessible tissue: Zhenshan97 flag leaf, score: 53.795	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0221873638	NA	6.87E-07	mr1305	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
vg0221873638	NA	2.22E-06	mr1586	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
vg0221873638	NA	9.71E-11	mr1714	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
vg0221873638	NA	3.53E-06	mr1246_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
vg0221873638	4.97E-06	6.44E-07	mr1305_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
vg0221873638	NA	2.39E-16	mr1592_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
vg0221873638	NA	1.93E-10	mr1595_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
vg0221873638	NA	5.49E-09	mr1600_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
vg0221873638	NA	1.24E-06	mr1691_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
vg0221873638	NA	4.05E-08	mr1783_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
vg0221873638	NA	2.56E-09	mr1947_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