One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
Fig 10
Impact of reference choice on phylogenetic trees of P. aeruginosa.
ML trees included the selected reference sequences of P. aeruginosa and the consensus sequences obtained from mappings against strains (A) M18 and (B) 12939. Reference M18 and isolate P5M1 (yellow) alter their phylogenetic relationships depending on reference choice.