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Detailed information for vg0138754938:

Variant ID: vg0138754938 (JBrowse)Variation Type: INDEL
Chromosome: chr01Position: 38754938
Reference Allele: GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCAAlternative Allele: G
Primary Allele: GTTCAATTCGCTCACTCAAT ACCAGTGAAAATATTAATTA CCASecondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


AGTCAGTTTACATTCTGATGAGTATCAGAAACCTCTCTGAATTGAGGTGATAAGTAATAGATGTTTGTCTTAACATGTTCAAATTATACCTGGGAAAAAA[GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA/G]
TTTACCAGGTCATGATTTCGTTCTAAATCAACAAGACCAGCAGATCAGCAAGTAACCTTGTGCAAATCCCAGGACATCTTACGAACCAACGTATCACGTA

Reverse complement sequence

TACGTGATACGTTGGTTCGTAAGATGTCCTGGGATTTGCACAAGGTTACTTGCTGATCTGCTGGTCTTGTTGATTTAGAACGAAATCATGACCTGGTAAA[TGGTAATTAATATTTTCACTGGTATTGAGTGAGCGAATTGAAC/C]
TTTTTTCCCAGGTATAATTTGAACATGTTAAGACAAACATCTATTACTTATCACCTCAATTCAGAGAGGTTTCTGATACTCATCAGAATGTAAACTGACT

Allele Frequencies:

Populations Population SizeFrequency of GTTCAATTCGCTCACTCAAT ACCAGTGAAAATATTAATTA CCA(primary allele) Frequency of G(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 95.30% 4.70% 0.00% 0.00% NA
All Indica  2759 97.80% 2.20% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 40.10% 59.90% 0.00% 0.00% NA
Indica I  595 95.00% 5.00% 0.00% 0.00% NA
Indica II  465 99.80% 0.20% 0.00% 0.00% NA
Indica III  913 98.10% 1.90% 0.00% 0.00% NA
Indica Intermediate  786 98.30% 1.70% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 100.00% 0.00% 0.00% 0.00% NA
Japonica Intermediate  241 100.00% 0.00% 0.00% 0.00% NA
VI/Aromatic  96 100.00% 0.00% 0.00% 0.00% NA
Intermediate  90 97.80% 2.20% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66720.1 splice_region_variant ; LOW silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66720.1 3_prime_UTR_variant ; 84.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66740.1 upstream_gene_variant ; 4818.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66710.1 downstream_gene_variant ; 4171.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66720.1 downstream_gene_variant ; 0.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66730.1 downstream_gene_variant ; 119.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66730.2 downstream_gene_variant ; 147.0bp to feature; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66720-LOC_Os01g66730 intergenic_region ; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N
vg0138754938 GTTCAATTCGCTCACTCAATACCAGTGAAAATATTAATTACCA -> G LOC_Os01g66720.1 non_coding_transcript_variant ; MODIFIER silent_mutation Average:66.957; most accessible tissue: Callus, score: 80.69 N N N N