Table 2. Sensitivity and specificity of COMET to detect and identify synthetic recombinants.

Insert size	n	URF found	Composition found
100	118 508	84.5%	84.1%
200	59 254	96.9%	96.8%
300	57 876	98.7%	98.7%
400	57 876	99.6%	99.6%
600	56 498	99.9%	99.9%
800	55 120	100.0%	100.0%
	Mean	96.6%	96.5%

A synthetic recombination data set was generated by replacing DNA sequences by the same sequence from another subtype. Different sizes of insert (from 100 bp to 800 bp) were introduced throughout the genome, generating 405 132 different recombinants. In the table, ‘URF found’ means that COMET recognized the sequence as ‘UNASSIGNED’. ‘Composition found’ means that COMET correctly identified the subtypes composing the background and the insert.