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For non-coding sites 4% could be explained by missed indels, 93% were in reads that had low mapping quality scores and/or were orphan pairs, suggesting that the read could have been misaligned, and 3% appeared truly homozygous.
Out of 240 coding sites examined, 53% were caused by indels that were too large for maq to properly align the reads, 36% were in reads that had low mapping quality scores and/or were orphan pairs, suggesting that the read could have been misaligned, 9% appeared truly homozygous, and 2% could not be explained.
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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