u/Hopeful_Bumblebee663

I ran the 20 P aeruginosa whole genome assemblies that I am using in my phylogenetic tree through check M2 on galaxy server. All of them have high completeness (99-100%) except for one which is 90%. The contamination value is <1% for all strains. However, some strains have N50 value < 100 kbp despite having high completeness. Should I be skipping these strains from my analysis?