SRP470062 PRJNA1035442 Large-scale duplication events underpin population-level flexibility in tRNA gene copy number in bacteria A set of four co-localized tRNA genes (gluTTC-glyGCC-gluTTC-glyGCC) weredeleted from the bacterium Pseudomonas fluorescens SBW25 by scar-free genetic engineering.To compensate for the resulting fitness drop, this engineered deletion genotype was evolved via serial transfer in rich medium (King's Medium B) for a period of 28 days (approximately 200 generations). Here, we provide the NGS data for population-level whole genome re-sequencing of several day-28 samples. There are a total of nine population samples: three independent populations founded by the engineered deletion mutant (M1-M3), five independent control populations founded by SBW25 wildtype (W1-W5), and a control day-0 SBW25 wildtype sample.