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Note that such an estimate of the alignment error rate may be underestimated because wrongly aligned human reads tend to be related to repetitive sequences in human and to be mapped back to the human sequences.
Had the rebels helped themselves to shopkeepers' goods because they believed they were wrongly aligned?
He has wrongly aligned his aspirations for a seven-day service to delivering the junior doctors' contract.
The mapping quality of the wrongly aligned pieces on these reads is only 2.4 (maximum 11), implying that BWA-SW is aware that these chimera are unreliable.
For the non-anchor positions, we know that some proportion is wrongly aligned in at least one of the (m 2 ) OPAs.
While some of these were legitimate human reads, there were probably also a similar amount of mouse reads not wrongly aligned to the human reference.
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For example, BWA wrongly aligns 11 reads out of 1 569 108 simulated 70 bp reads mapped with mapping quality 60.
If your hips are wider than your waist (usually is), it creates a gap, and gravity fills the gap by wrongly aligning the spine.
The alignments were manually inspected and edited in Jalview 2.7 in order to curate wrongly predicted sequences and adjust poorly aligned sequence stretches.
Secondly, we obtained the quality statistics of read libraries such as read coverage aligned across the genome, proportions of wrongly oriented mapped reads and searched for potential biases due to GC content, repeat composition of the C. elegans genome and the different insert size libraries.
In other cases, one of the calls in the two genomes was wrongly reported due to ambiguity in the alignments (i.e. the reads could have been aligned differently, so that the position of a variant differed between the genomes, even though the resulting non-reference sequence was the same).
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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