Search for Variation information by Variation ID:

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

Detailed information for vg0110693719:

Variant ID: vg0110693719 (JBrowse)	Variation Type: SNP
Chromosome: chr01	Position: 10693719
Reference Allele: G	Alternative Allele: T
Primary Allele: G	Secondary Allele: T

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ACATAGCTGAGAAGACCCTCTCAACTGAAGCCGTTGCCACCGGAAGTATCAATGATAACTCAATGAGCCTATACACCAAGTGATAAGTTCTATTCTTTCC[G/T]
GTTTGAACCATTAATTCAGCAACCTTTGCAAGATCTTTACATCCAAGAAATTCTTTACTTCTCCTAACATTGCTAATAAAATTTCCAAGTTGAGTTCGTA

Reverse complement sequence

TACGAACTCAACTTGGAAATTTTATTAGCAATGTTAGGAGAAGTAAAGAATTTCTTGGATGTAAAGATCTTGCAAAGGTTGCTGAATTAATGGTTCAAAC[C/A]
GGAAAGAATAGAACTTATCACTTGGTGTATAGGCTCATTGAGTTATCATTGATACTTCCGGTGGCAACGGCTTCAGTTGAGAGGGTCTTCTCAGCTATGT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of T(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	72.90%	1.50%	18.41%	7.17%	NA
All Indica	2759	56.40%	2.50%	29.58%	11.53%	NA
All Japonica	1512	99.00%	0.00%	0.53%	0.46%	NA
Aus	269	82.90%	0.00%	13.01%	4.09%	NA
Indica I	595	62.90%	0.00%	30.25%	6.89%	NA
Indica II	465	48.60%	3.20%	35.27%	12.90%	NA
Indica III	913	53.00%	3.40%	28.81%	14.79%	NA
Indica Intermediate	786	60.10%	2.90%	26.59%	10.43%	NA
Temperate Japonica	767	99.10%	0.00%	0.13%	0.78%	NA
Tropical Japonica	504	99.00%	0.00%	0.99%	0.00%	NA
Japonica Intermediate	241	98.80%	0.00%	0.83%	0.41%	NA
VI/Aromatic	96	97.90%	1.00%	1.04%	0.00%	NA
Intermediate	90	83.30%	2.20%	11.11%	3.33%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0110693719	G -> T	LOC_Os01g18920.1	synonymous_variant ; p.Thr703Thr; LOW	synonymous_codon	Average:5.704; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N
vg0110693719	G -> DEL	LOC_Os01g18920.1	N	frameshift_variant	Average:5.704; most accessible tissue: Zhenshan97 root, score: 12.891	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0110693719	4.57E-06	NA	mr1224_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