KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Klenow fragment exo−	New England Biolabs	M0212S
MyOne Streptavidin C1 Dynabeads	Life Technologies	65001
Critical commercial assays
PureLink Genomic DNA Mini kit	Life Technologies	K210011
LTP Library Preparation Kit	Kappa Biosystems	Kk8232
SeqCap EZ Hybridization and Wash Kit	NimbleGen	05 634 261 001
KAPA Library Amplification Kit	Kappa Biosystems	KK2611
Deposited data
Raw Illumina Sequencing Data	This paper	NCBI SRA: PRJNA601748
Experimental models: Organisms/strains
E. coli: Strain background: REL606	Lenski et al., 1991	N/A
E. coli: Strain background: REL607	Lenski et al., 1991	N/A
Oligonucleotides
21 Illumina Sequencing Adapters containing 12-base MI: See Table S1	This paper	N/A
242 60-base xGen Lockdown probes: see Table S2	This paper	N/A
2 Blocking Oligos: see Table S3	This paper	N/A
Software and algorithms
BLASTN	Camacho et al., 2009	https://blast.ncbi.nlm.nih.gov/Blast.cgi
CSR generation python script	This paper	DOI: 10.5281/zenodo.5092871
Stacks v1.48	Catchen et al., 2013	https://catchenlab.life.illinois.edu/stacks/
breseq v0.26.0	Deatherage and Barrick, 2014	https://github.com/barricklab/breseq
Bowtie2 v2.2.5	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
R v4.0.0	R Core Team, 2016	https://www.r-project.org/
Custom breseq post-processing Python script	This paper	DOI: 10.5281/zenodo.5092871
Statistical testing and modeling of trajectories R script	This paper	DOI: 10.5281/zenodo.5092871
Pymol v2.3.5	Schrodinger LLC	Pymol.org
Pymol figure visualization script	This paper	DOI: 10.5281/zenodo.5092871
Other
REL606.6.GENES.1400-flanking.gff3	This paper	DOI: 10.5281/zenodo.5092871
REL606.6.GENES.MASKED.gff3	This paper	DOI: 10.5281/zenodo.5092871