One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads
Fig 8
Impact of reference choice on phylogenetic trees of L. pneumophila.
ML trees included the selected reference sequences of L. pneumophila and the consensus sequences obtained from mappings against strains (A) Philadelphia 1, (B) Paris, (C) Alcoy and (D) Lansing 3. Clusters of isolates related with references Paris (red) and Alcoy (blue) are coloured in the first three phylogenies. Isolates 28HGV and 91HGV (highlighted in yellow) were placed in different clades in the trees when using references Paris and Alcoy. Clade of references resulting from using Lansing 3 as reference genome is coloured in red.