Search for Variation information by Variation ID:

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

Detailed information for vg0426093766:

Variant ID: vg0426093766 (JBrowse)Variation Type: INDEL
Chromosome: chr04Position: 26093766
Reference Allele: CAAAAAlternative Allele: CAAA,CAA,CA,C
Primary Allele: CAAASecondary Allele: CAAAA

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGAAATCAATAGCTAATGTTTCTATTCATGACGTGTCTACCAGGGAGGATTTACATAATTAGAGTCGGGGACTTTTTTGGGGCCTTTTGTGGGTTGACTC[CAAAA/CAAA,CAA,CA,C]
AAAAAAAAAAAATCCCAATGAGAACCTTTAAAAAAAACAGAATGATCTATTTTGGTTTACTTAATGATCAATGCGCCTATGATTGCATGCATCTGTTGAA

Reverse complement sequence

TTCAACAGATGCATGCAATCATAGGCGCATTGATCATTAAGTAAACCAAAATAGATCATTCTGTTTTTTTTAAAGGTTCTCATTGGGATTTTTTTTTTTT[TTTTG/TTTG,TTG,TG,G]
GAGTCAACCCACAAAAGGCCCCAAAAAAGTCCCCGACTCTAATTATGTAAATCCTCCCTGGTAGACACGTCATGAATAGAAACATTAGCTATTGATTTCT

Allele Frequencies:

Populations Population SizeFrequency of CAAA(primary allele) Frequency of CAAAA(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 33.70% 22.10% 36.29% 1.67% CAA: 5.69%; CA: 0.40%; C: 0.11%
All Indica  2759 38.00% 17.50% 39.14% 2.86% CAA: 1.99%; CA: 0.51%
All Japonica  1512 28.80% 30.40% 29.70% 0.00% CAA: 10.78%; C: 0.26%; CA: 0.07%
Aus  269 20.40% 18.20% 42.75% 0.00% CAA: 17.47%; CA: 1.12%
Indica I  595 41.00% 17.10% 35.80% 3.03% CAA: 2.52%; CA: 0.50%
Indica II  465 36.60% 15.10% 42.37% 4.95% CAA: 0.65%; CA: 0.43%
Indica III  913 40.40% 18.10% 38.44% 0.99% CAA: 1.86%; CA: 0.22%
Indica Intermediate  786 33.80% 18.40% 40.59% 3.69% CAA: 2.54%; CA: 0.89%
Temperate Japonica  767 11.30% 47.50% 26.73% 0.00% CAA: 14.34%; CA: 0.13%
Tropical Japonica  504 51.80% 9.50% 32.54% 0.00% CAA: 5.75%; C: 0.40%
Japonica Intermediate  241 36.50% 19.50% 33.20% 0.00% CAA: 9.96%; C: 0.83%
VI/Aromatic  96 30.20% 28.10% 39.58% 0.00% CA: 1.04%; CAA: 1.04%
Intermediate  90 27.80% 31.10% 36.67% 0.00% CAA: 3.33%; C: 1.11%

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0426093766 CAAAA -> CA LOC_Os04g44030.1 3_prime_UTR_variant ; 1623.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> CA LOC_Os04g44050.1 upstream_gene_variant ; 3941.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> CAA LOC_Os04g44030.1 3_prime_UTR_variant ; 1624.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> CAA LOC_Os04g44050.1 upstream_gene_variant ; 3940.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> CAAA LOC_Os04g44030.1 3_prime_UTR_variant ; 1625.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> CAAA LOC_Os04g44050.1 upstream_gene_variant ; 3939.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> DEL N N silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> C LOC_Os04g44030.1 3_prime_UTR_variant ; 1620.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N
vg0426093766 CAAAA -> C LOC_Os04g44050.1 upstream_gene_variant ; 3942.0bp to feature; MODIFIER silent_mutation Average:48.008; most accessible tissue: Callus, score: 84.682 N N N N