Search for Variation information by Variation ID:

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

Detailed information for vg1105183890:

Variant ID: vg1105183890 (JBrowse)	Variation Type: INDEL
Chromosome: chr11	Position: 5183890
Reference Allele: G	Alternative Allele: GTGGAGACTTA
Primary Allele: G	Secondary Allele: GTGGAGACTTA

Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 0.98, others allele: 0.00, population size: 53. )

Flanking Sequence (100 bp) in Reference Genome:

GACTAAATCCCATCCTGACCATAAGATGCGTGACTTCGGTGCAGACTTTTTTCTTTGGGCATGTGATATTACTGATGTTTGGGGTCTTAGGGGCTGTTTG[G/GTGGAGACTTA]
TTTCCAGGGACTTATTCCAATTCCATGTCACATCGGATGTTTGGATACTAATTTGGAGTATTAAACATACACTAATTACAAAACACATTCCATATCCTTG

Reverse complement sequence

CAAGGATATGGAATGTGTTTTGTAATTAGTGTATGTTTAATACTCCAAATTAGTATCCAAACATCCGATGTGACATGGAATTGGAATAAGTCCCTGGAAA[C/TAAGTCTCCAC]
CAAACAGCCCCTAAGACCCCAAACATCAGTAATATCACATGCCCAAAGAAAAAAGTCTGCACCGAAGTCACGCATCTTATGGTCAGGATGGGATTTAGTC

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of GTGGAGACTTA(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	10.00%	0.40%	3.70%	85.87%	NA
All Indica	2759	0.90%	0.10%	4.39%	94.56%	NA
All Japonica	1512	28.20%	0.70%	2.18%	68.85%	NA
Aus	269	0.70%	1.50%	5.58%	92.19%	NA
Indica I	595	2.40%	0.20%	0.34%	97.14%	NA
Indica II	465	0.40%	0.00%	0.22%	99.35%	NA
Indica III	913	0.10%	0.00%	10.08%	89.81%	NA
Indica Intermediate	786	1.00%	0.40%	3.31%	95.29%	NA
Temperate Japonica	767	33.80%	0.50%	0.78%	64.93%	NA
Tropical Japonica	504	14.10%	1.40%	0.40%	84.13%	NA
Japonica Intermediate	241	40.20%	0.00%	10.37%	49.38%	NA
VI/Aromatic	96	4.20%	0.00%	3.12%	92.71%	NA
Intermediate	90	17.80%	0.00%	3.33%	78.89%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1105183890	G -> GTGGAGACTTA	LOC_Os11g09710.1	frameshift_variant ; p.Ser323fs; HIGH	frameshift_variant	Average:19.337; most accessible tissue: Callus, score: 53.099	N	N	N	N
vg1105183890	G -> DEL	LOC_Os11g09710.1	N	frameshift_variant	Average:19.337; most accessible tissue: Callus, score: 53.099	N	N	N	N