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Using this pipeline we identified two putative alternative loci for known miRNAs, and 11 new miRNAs.
Moreover, because conifer genomes are very large, the genetic linkage within our full-sib family likely extends over numerous genes that, due to the limited statistical power of the S+A-set, all could be considered as alternative loci for the QTL.
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On the other hand, the alternative locus for miRNA transcription can ensure that the fast concentration shifts required by the differentiation program are achieved, specifically via non-linear response of the target to even modest surges in the miRNA transcription rate.
For homozygote alternative loci, SNV concordance approached 100% for SAM, UG and HC, with slightly lower concordance observed in PL.Genotype concordance was very high in both single and multi sample results; depending on software, genotype concordance for single sample results was between 99.2-99.3% and between 99.1-99.3% for multi sample methods.
The presence of alternative loci in iJN746 explains partial disagreement for argA, argE, ilvA, and argJ.
The alignment and corresponding single-gene tree characteristics (see below) served as a basis for several alternative locus selection strategies.
An alternative locus specific method with improved reliability for CNV determination is the paralogue ratio test (PRT) [ 8].
In the case of Okanagan Lake kokanee, an outlier-based approach may offer the only alternative to neutral loci for informing fisheries management.
The use of outlier loci constitutes a promising alternative to neutral loci for informing fisheries management of recently diverged stocks, particularly for enhancing stock assessment, long-term ecological monitoring, and evaluation of current management practices.
As a result, we adopted a different strategy and retained as outliers those loci for which alternative phenotypes (fragment presence/absence) were fixed or nearly fixed in each strain.
Only when the information content of a selected locus within a cross was low, was an alternative flanking locus chosen for that cross.
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