It is unclear whether this highly unusual ORF is a sequencing artifact, a pseudogene, or whether it is actually expressed.
It is possible that the described mutation is a sequencing artifact, as conservation of a processed pseudogene in the possum is unlikely.
It is unlikely that this result is a sequencing artifact: the full length of most tRNAs is 75 90 nt, and the sequencing runs used to generate these data were 50 cycles while the reads occupy a narrow size range of 30 33 nt.
Our alignment free analysis of this indel agrees with the authors' conclusions despite there being a sequence artifact in their original alignment [ 11].
We assume that one of the PTVs is actually a sequencing artifact and that the trait value of the corresponding individual is drawn from a standard normal distribution.
This variant is likely a sequencing artifact because of its frequency in both populations and our inability to confirm it by Sanger sequencing (data not shown).
As no individual was scored unambiguously as a thymidine, we could not rule out the possibility that the ambiguity was due to a sequencing artifact, and this position was excluded from the haplotype reconstruction.
Assuming it is not just a sequencing artifact, how this gene originated, i. e. whether simply emerged in a Batrachochytrium-specific duplication followed by drastic sequence changes or, perhaps, by horizontal transmission from another, unknown organism, is uncertain.
We also identified an inflated frequency of SNPs at the G base of the canonical AG acceptor site which has been previously identified as a sequencing artifact [ 48].
Because all of the sequences presented here are consensus results, generated from multiple PCRs and multiple clones sequenced on both strands, the difference in the database for modern samples is best interpreted as a sequencing artifact in the published sequences.
