Here, we traced genetic variation (based on sequence variants in the internal transcribed spacer region, ITS) among seven geographically isolated populations of the ichthyosporean Caullerya mesnili, a common microparasite of the cladoceran Daphnia (here, the D. longispina hybrid complex).
Based on sequence conservation, human variants can be tested by introducing homologous mutations in the yeast ortholog.
Furthermore, the Obp proteins were present also in less intense spots but their identification was based on sequence regions identical for all variants not allowing correct determination of the particular variant and they are not further discussed in this study.
Based on sequence comparison, two highly similar variants were classified as subtype GHV-1, whereas the third variant represents subtype GHV-2.
Eleven sequence variants (two in BRCA1 and nine in BRCA2) may be potentially damaging based on sequence conservation and Grantham score, and five sequence variants are unlikely to be clinically relevant.
Using a binning procedure, readDepth calls copy number variants based on sequence depth, and then invokes a circular binary segmentation algorithm to call segment boundaries.
Taken together, use of primer variants based on sequence variations of HML-2 loci significantly increases the number of amplifiable loci.
The readDepth uses a binning procedure to call copy number variants based on sequence depth and then call segment boundaries using a circular binary segmentation algorithm.
We removed variant calls based on sequence reads with multiple differences from the reference as well as at positions where more than a quarter of the reads in both isolates carried the variant call.
As shown in Figure 4A, the number of CCHC arrays in NC varies depending on the Ty3/Gypsy lineage and the Retroviridae class (links in red), and both the flap and the GPY/F motifs delineate multiple variant motifs based on sequence polymorphisms preserved similarly (links in black and blue, respectively).
