Alignment of a read generated from GU570202 against ADD46842. The figure illustrates the HAXAT alignment of a Titanium read generated from ORF1 of GU570202 aligned against ADD46842. Five frame-shift corrections were found and are highlighted in red and with lower case characters. The first correction, the “c”, is aligned against a corresponding database position and is therefore regarded as an inserted nucleotide (predicted undercall). The next consequent correction, the first “g” is aligned against a database gap and is thus a deleted nucleotide (predicted overcall). The alignment is produced using BLOSUM62, a gap open/ext cost of 8/2 as well as a single/double nucleotide gap cost of 16/28 and the homopolymer parameters “h = 0.5 and t = 4” (default parameters).
Lysholm BMC Bioinformatics 2012 13:230 doi:10.1186/1471-2105-13-230