One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
Fig 9
Impact of reference choice on phylogenetic trees of K. pneumoniae.
ML trees included the selected reference sequences from K. pneumoniae and the consensus sequences obtained from mappings against strains (A) HS11286 and (B) NTUH-K2044. Isolates HGV2C-06 and HCV1-10 (yellow) changed their placement depending on reference choice.