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Secondary reads that do not have a best match to a unique defined locus are discarded.
Reads in a stack are primary reads, and reads that are set aside are secondary reads.
At the end of this stage, Stacks has constructed a set of putative loci from high-confidence unique stacks and has buttressed locus depth by adding secondary reads.
Secondary reads (2° reads, Figure 1E) that were set aside earlier are now matched against putative loci using the k-mer search algorithm but with greater nucleotide distance (two nucleotides larger than the within-individual distance parameter by default).
Apart from the threshold issue, while considering secondary reads in the mtDNA (heteroplasmy) one should apply several filters such as 'no strand bias', unique mapping (NuMT exclusion) and 'exclusion of mutations at the end of reads'.
We report results using an optimum coverage of 15 reads per individual (excluding all stacks with a lower coverage), a maximum of two mismatches between reads for a single individual as well as allowing four mismatches between primary and secondary reads within ustacks.
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The linebackers and secondary read Collins like a grade-school book, tying a Super Bowl record by intercepting four of his passes.
Norene Mahoney Rolle Auburndale, Mass., March 23, 2009 The writer is a secondary reading specialist.
Miranda Carter tells it straight, with assiduous reporting based on interviews and secondary reading.
Most literary criticism, whether academic or journalistic, is ideally geared up for "secondary reading" – by which I mean all that stuff that requires us to generate some kind of secondary text – a commentary, an exegesis, a review and so on.
To the Editor: As someone who spent four years working as a secondary reading specialist in a struggling public high school in California, I am familiar with the problems that arise when students cannot read at grade level.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com