Search for Variation information by Variation ID:

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

Detailed information for vg0401332098:

Variant ID: vg0401332098 (JBrowse)	Variation Type: SNP
Chromosome: chr04	Position: 1332098
Reference Allele: C	Alternative Allele: T
Primary Allele: C	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATTTCCCCAAGCATGGATTAATTACTCCTTGTATCATGTTAAAACCAAGGCTTAGATATTTTAGTTGATGGAGGCCACAAATACCTGTGTACATTGGAGC[C/T]
GGAGCCACATGTTACTAATTGATATAGTTTCAACATGCGAAAATTAAAAAGATCAAATGATGAGTTGATTTGAAGGAATTGACCTTCTATATTTTCCTTT

Reverse complement sequence

AAAGGAAAATATAGAAGGTCAATTCCTTCAAATCAACTCATCATTTGATCTTTTTAATTTTCGCATGTTGAAACTATATCAATTAGTAACATGTGGCTCC[G/A]
GCTCCAATGTACACAGGTATTTGTGGCCTCCATCAACTAAAATATCTAAGCCTTGGTTTTAACATGATACAAGGAGTAATTAATCCATGCTTGGGGAAAT

Allele Frequencies:

Populations	Population Size	Frequency of C(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	74.80%	13.10%	0.28%	11.85%	NA
All Indica	2759	86.00%	12.60%	0.18%	1.16%	NA
All Japonica	1512	69.40%	0.30%	0.46%	29.83%	NA
Aus	269	3.70%	91.80%	0.00%	4.46%	NA
Indica I	595	88.60%	10.40%	0.00%	1.01%	NA
Indica II	465	96.10%	3.40%	0.00%	0.43%	NA
Indica III	913	78.20%	19.80%	0.00%	1.97%	NA
Indica Intermediate	786	87.30%	11.30%	0.64%	0.76%	NA
Temperate Japonica	767	59.50%	0.30%	0.52%	39.77%	NA
Tropical Japonica	504	79.00%	0.00%	0.20%	20.83%	NA
Japonica Intermediate	241	80.90%	1.20%	0.83%	17.01%	NA
VI/Aromatic	96	24.00%	15.60%	1.04%	59.38%	NA
Intermediate	90	85.60%	5.60%	0.00%	8.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0401332098	C -> DEL	N	N	silent_mutation	Average:29.162; most accessible tissue: Callus, score: 45.629	N	N	N	N
vg0401332098	C -> T	LOC_Os04g03180.1	intron_variant ; MODIFIER	silent_mutation	Average:29.162; most accessible tissue: Callus, score: 45.629	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0401332098	NA	6.35E-06	mr1052	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
vg0401332098	1.20E-06	NA	mr1033_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