Search for Variation information by Variation ID:

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

Detailed information for vg0226923436:

Variant ID: vg0226923436 (JBrowse)	Variation Type: SNP
Chromosome: chr02	Position: 26923436
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.72, A: 0.29, others allele: 0.00, population size: 318. )

Flanking Sequence (100 bp) in Reference Genome:

TCTCCCGTCCACTGACGGTATAACCAGACAAGGCTGCATTCCATGTTTCTGCACGCCATGAGCCCCTCTCAAGTGTTAATCTCATCAGCTTCATCTTACC[G/A]
CACCTCGCATAAGCGTCGATAAGCGCAGTTTCAACAGCAATGTCTGATTTAAGGCCAAGTCTAATGCAGAGTGCATGTGTGCACTTGGCATGCTTCCCTG

Reverse complement sequence

CAGGGAAGCATGCCAAGTGCACACATGCACTCTGCATTAGACTTGGCCTTAAATCAGACATTGCTGTTGAAACTGCGCTTATCGACGCTTATGCGAGGTG[C/T]
GGTAAGATGAAGCTGATGAGATTAACACTTGAGAGGGGCTCATGGCGTGCAGAAACATGGAATGCAGCCTTGTCTGGTTATACCGTCAGTGGACGGGAGA

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	63.50%	36.10%	0.08%	0.25%	NA
All Indica	2759	97.40%	2.20%	0.07%	0.25%	NA
All Japonica	1512	0.70%	98.90%	0.13%	0.26%	NA
Aus	269	97.40%	2.60%	0.00%	0.00%	NA
Indica I	595	98.30%	1.70%	0.00%	0.00%	NA
Indica II	465	97.80%	1.70%	0.00%	0.43%	NA
Indica III	913	98.60%	1.30%	0.00%	0.11%	NA
Indica Intermediate	786	95.20%	4.10%	0.25%	0.51%	NA
Temperate Japonica	767	0.30%	99.50%	0.13%	0.13%	NA
Tropical Japonica	504	1.60%	98.00%	0.20%	0.20%	NA
Japonica Intermediate	241	0.00%	99.20%	0.00%	0.83%	NA
VI/Aromatic	96	4.20%	95.80%	0.00%	0.00%	NA
Intermediate	90	42.20%	56.70%	0.00%	1.11%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0226923436	G -> A	LOC_Os02g44480.1	synonymous_variant ; p.Cys258Cys; LOW	synonymous_codon	Average:74.215; most accessible tissue: Callus, score: 83.021	N	N	N	N
vg0226923436	G -> DEL	LOC_Os02g44480.1	N	frameshift_variant	Average:74.215; most accessible tissue: Callus, score: 83.021	N	N	N	N