Exclusion stage	Family (as labelled)	Species	Accession	Assembly level
cytb family-discordant	Emballonuridae	Rhynchonycteris naso	GCA_037038545.1	Chromosome
cytb family-discordant	Mormoopidae	Pteronotus mesoamericanus	GCF_021234165.1	Scaffold
cytb family-discordant	Mormoopidae	Pteronotus davyi	GCA_058219175.1	Chromosome
LTR index intractable	Miniopteridae	Miniopterus natalensis	GCA_054644295.1	Chromosome
LTR index intractable	Miniopteridae	Miniopterus schreibersii	GCF_964146895.1	Chromosome
LTR index intractable	Rhinolophidae	Rhinolophus affinis	GCA_043728065.1	Chromosome
LTR index intractable	Vespertilionidae	Pipistrellus hanaki	GCF_964339955.1	Chromosome
LTR index intractable	Vespertilionidae	Myotis nattereri	GCF_964212035.1	Chromosome