Search for Variation information by Variation ID:

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

Detailed information for vg0113669388:

Variant ID: vg0113669388 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 13669388
Reference Allele: A	Alternative Allele: G
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACACCAGTTAAGAATTTAGAGTCTAGCCAAGTGTAATACATGTCCCGGTGCTCAATAACCGCGAGCACGGCTATTCGAATAGATTTGGTTTACTCACACT[A/G]
CAGTGGATGTACACTTTACCCACACTCCGCGACTGCCCAACACATGAGCCTCGTCTCAACACATGAAACGTGTCACGGCAAAGCTTTTCGATAACCTCGC

Reverse complement sequence

GCGAGGTTATCGAAAAGCTTTGCCGTGACACGTTTCATGTGTTGAGACGAGGCTCATGTGTTGGGCAGTCGCGGAGTGTGGGTAAAGTGTACATCCACTG[T/C]
AGTGTGAGTAAACCAAATCTATTCGAATAGCCGTGCTCGCGGTTATTGAGCACCGGGACATGTATTACACTTGGCTAGACTCTAAATTCTTAACTGGTGT

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	42.20%	0.60%	34.85%	22.32%	NA
All Indica	2759	22.00%	1.00%	49.62%	27.40%	NA
All Japonica	1512	84.00%	0.00%	1.79%	14.22%	NA
Aus	269	14.10%	0.00%	72.49%	13.38%	NA
Indica I	595	8.10%	1.20%	51.76%	38.99%	NA
Indica II	465	17.40%	0.00%	40.65%	41.94%	NA
Indica III	913	33.00%	1.40%	52.46%	13.14%	NA
Indica Intermediate	786	22.40%	1.00%	50.00%	26.59%	NA
Temperate Japonica	767	97.10%	0.00%	0.13%	2.74%	NA
Tropical Japonica	504	60.30%	0.00%	4.76%	34.92%	NA
Japonica Intermediate	241	91.70%	0.00%	0.83%	7.47%	NA
VI/Aromatic	96	33.30%	0.00%	29.17%	37.50%	NA
Intermediate	90	55.60%	0.00%	31.11%	13.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0113669388	A -> G	LOC_Os01g24260.1	synonymous_variant ; p.Cys139Cys; LOW	synonymous_codon	Average:6.128; most accessible tissue: Callus, score: 10.993	N	N	N	N
vg0113669388	A -> DEL	LOC_Os01g24260.1	N	frameshift_variant	Average:6.128; most accessible tissue: Callus, score: 10.993	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0113669388	3.56E-06	3.56E-06	mr1736	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