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Detailed information for vg0825997839:

Variant ID: vg0825997839 (JBrowse)Variation Type: INDEL
Chromosome: chr08Position: 25997839
Reference Allele: CTAlternative Allele: C
Primary Allele: CTSecondary Allele: C

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:


TGAAGAAGTCGAGGCACTTGCTCTTCAGCTCCGGGCAGCCGTGCATCTCGGCGCAGCCCAGCGTCGTCGCCACCGTCTCCACTGACACGCTCTCCCACAG[CT/C]
TCTGGGCGCACATCAGCTTCAGCCCGTCCAGCGCGTACCTGTCCGCCGCCGCGAGCAAACGCTGATGATGAAGCAGATGATCGCTCGTGCTCGCCGTCGT

Reverse complement sequence

ACGACGGCGAGCACGAGCGATCATCTGCTTCATCATCAGCGTTTGCTCGCGGCGGCGGACAGGTACGCGCTGGACGGGCTGAAGCTGATGTGCGCCCAGA[AG/G]
CTGTGGGAGAGCGTGTCAGTGGAGACGGTGGCGACGACGCTGGGCTGCGCCGAGATGCACGGCTGCCCGGAGCTGAAGAGCAAGTGCCTCGACTTCTTCA

Allele Frequencies:

Populations Population SizeFrequency of CT(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 98.80% 1.20% 0.00% 0.00% NA
All Indica  2759 97.90% 2.10% 0.00% 0.00% NA
All Japonica  1512 100.00% 0.00% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 100.00% 0.00% 0.00% 0.00% NA
Indica II  465 93.30% 6.70% 0.00% 0.00% NA
Indica III  913 97.70% 2.30% 0.00% 0.00% NA
Indica Intermediate  786 99.20% 0.80% 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  90 100.00% 0.00% 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
vg0825997839 CT -> C LOC_Os08g41150.1 frameshift_variant ; p.Lys287fs; HIGH frameshift_variant Average:67.492; most accessible tissue: Zhenshan97 panicle, score: 84.824 N N N N