Exact(1)
Alignment is at the center distance of the array.
Similar(7)
Merging was launched if the alignment was at least of 15 nucleotides, with less than 4 mismatches and an identity percent of at least 90%.
A read was annotated as an insertion sequence according to the best BLAST hit if (1) the hit had a sequence similarity above 80% and (2) if the alignment was at least 50 bases.
A single strong blast detected sequence similarity was defined as E-value for the best blast alignment being at least 106 times lower than the E-value for the second best blast alignment.
Sequences were clustered using the vmatch program -dbcluster option, requiring clustered sequences to show mutual 85% identity, and the alignments be at least 20 bases long.
Reads were considered to have indels if their alignments were at least 53 nt long and had any gaps.
Reads were considered non-indels if their alignments were at least 53 nucleotides long without any gaps.
Almost all the nucleotide discrepancies in the 24/25 alignments were at the SNP sites, which is an encouraging in silico validation of these SNPs.
Related(1)
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com