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> We observed an increased frequency of premature stop codon predictions near the start and end positions of the C. intestinalis A reference sequence in Ensembl, which probably reflects annotation errors or true biological variation.
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This indicator variable could be defined to reflect annotation and/or frequency.
This was taken to reflect annotation errors rather than true gene duplication events.
This 'masking' scheme may reflect annotation and/or frequency, so that only coding or non-synonymous variants are included in the analysis, for example, for some pre-specified MAF threshold.
This article reflects the annotation set as of the FB2014_06, Dmel annotation release 6.03 (R6.03).
The number of protein sequence entries reflects the annotation of ORFs at the time of download.
We cannot rule out the possibility that this reflects an annotation bias, due to difficulties in viewing and collating transcriptional feature evidence over larger distances.
We used Reflect annotation software [ 72] to identify disease names in the text.
The automatic updating of the inference, ensuring that UberPheno reflects current annotations (and definitions, which change less frequently) should be adopted as a 'best practice' by other providers of derived information.
Therefore, the utilities of the metrics are limited when considering species that have less comprehensive annotations, and the metrics may reflect potential annotation biases from the databases.
However, Cardinium cEper1 has almost no annotated pseudogenes, a difference that might reflect gene annotation criteria because open reading frames that belong to transposase fragments are annotated as coding sequences (CDSs).
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