Search for Variation information by Variation ID:

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

Detailed information for vg0421397191:

Variant ID: vg0421397191 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 21397191
Reference Allele: A	Alternative Allele: C
Primary Allele: A	Secondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 1.00, others allele: 0.00, population size: 359. )

Flanking Sequence (100 bp) in Reference Genome:

AATTATATTTCTTGTAACAATGCATCAACTTAATTAATTTGCGGCTCGCTCGATCAGTGTTACTTAGTTTATTTGTTCATCGATCTTTGAAAAAAAGAAG[A/C]
AGCAGTTCTACTGATTATATATCAAAACATCAATTGATTATATATGGTTGATGTAATTGTTGTGTATATGTGTGTAGGTGGCGAGTGGAATTGATCGGTT

Reverse complement sequence

AACCGATCAATTCCACTCGCCACCTACACACATATACACAACAATTACATCAACCATATATAATCAATTGATGTTTTGATATATAATCAGTAGAACTGCT[T/G]
CTTCTTTTTTTCAAAGATCGATGAACAAATAAACTAAGTAACACTGATCGAGCGAGCCGCAAATTAATTAAGTTGATGCATTGTTACAAGAAATATAATT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of C(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	94.80%	2.60%	0.08%	2.50%	NA
All Indica	2759	92.10%	4.40%	0.14%	3.37%	NA
All Japonica	1512	98.30%	0.00%	0.00%	1.65%	NA
Aus	269	100.00%	0.00%	0.00%	0.00%	NA
Indica I	595	90.10%	9.90%	0.00%	0.00%	NA
Indica II	465	95.30%	0.20%	0.43%	4.09%	NA
Indica III	913	92.30%	1.50%	0.00%	6.13%	NA
Indica Intermediate	786	91.30%	6.10%	0.25%	2.29%	NA
Temperate Japonica	767	99.90%	0.00%	0.00%	0.13%	NA
Tropical Japonica	504	95.40%	0.00%	0.00%	4.56%	NA
Japonica Intermediate	241	99.60%	0.00%	0.00%	0.41%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	98.90%	1.10%	0.00%	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
vg0421397191	A -> C	LOC_Os04g35210.1	intron_variant ; MODIFIER	silent_mutation	Average:66.705; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N
vg0421397191	A -> DEL	N	N	silent_mutation	Average:66.705; most accessible tissue: Zhenshan97 young leaf, score: 85.001	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0421397191	2.21E-06	1.70E-06	mr1134_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
vg0421397191	9.84E-06	1.99E-07	mr1672_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