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Exact(4)
This region was excluded from the analysis due to sequencing problems.
In addition, other TvBspA sequences have sequencing ambiguities or are obviously truncated due to sequencing problems or missing data.
Pika MVP was included in the ASR because this region of exon 9 was the only missing sequence and is more likely to be due to sequencing problems rather than the absence of this conserved region.
To allow for such indels but limit the number of deviations from the standard loop which could occur due to sequencing problems, we introduced the criteria that V3-loops had to have a length of at least 30 and at most 45 residues.
Similar(56)
The lack of the class-VI myosin might be a specific characteristic of Nasonia vitripennis, or due to sequencing and assembly problems, which are, however, unlikely given the high coverage of the Nasonia genome sequence.
Errors within a binary gene tree can be due to sequence alignment problems, phylogenetic reconstruction artifacts (e.g. long branch attraction) or a lack of phylogenetic signal (especially for genes encoded by short sequences).
Since the PCR and Southern data for this locus were unambiguous we are inclined to believe that, as mentioned earlier, the discrepancy between our data and AmoebaDB may be due to sequence assembly problems.
A direct negative correlation of the DS nucleosome occupancy and pol III occupancy/RNA yield from other gene cases could not be made due to sequence redundancy problems associated with isogenes as mentioned above, but the differences in relative RNA levels from genes with mostly similar pol III occupancy can most probably be correlated with the DS nucleosome occupancy, as discussed later.
However, as we obtained a high quality fully assembled genome, this fragment absence could not be due to sequencing errors or assembling problems.
This redundancy of the transcript catalogue is caused both by the assembly of contigs representing alternative splicing events and gene paralogs as well by assembly problems due to sequencing errors and repetitive motifs.
Since the additional variations were rare and not consistent across all reads, problems might have been due to sequencing or PCR aberrations rather than actual sequence polymorphism.
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