Table 2. Mutations fixed during long-term adaptation of ID8 and NC28 lineages.

Genotype	Protein function	Protein name	Aa position	$\text{Δ}\mathrm{Aa}$	Nuc. position	$\text{Δ}\mathrm{Nuc}$	First passage obs.
ID8wt1	Coat	F	77	I $\to$ T	2792	T $\to$ C	10
	DNA pilot	H	79	S $\to$ F	4762	C $\to$ T	20
	DNA packaging	C	65	I $\to$ V	1912	A $\to$ G	30
	DNA binding	J	15	A $\to$ V	2483	C $\to$ T	40
	Coat	F	312	Silent	3498	C $\to$ T	70
	DNA pilot	H	135	G $\to$ D	4930	G $\to$ A	70
ID8wt2	Scaffolding	D	45	A $\to$ S	2108	G $\to$ T	20
	Spike	G	65	T $\to$ A	4175	A $\to$ G	20
	DNA pilot	H	88	T $\to$ I	4789	C $\to$ T	30
	DNA pilot	H	173	G $\to$ E	5044	G $\to$ A	40
	DNA packaging	C	53	A $\to$ G	1877	A $\to$ G	70
ID8evol1	DNA pilot	H	91	C $\to$ G	4797	G $\to$ T	10
	Coat	F	12	L $\to$ P	2597	C $\to$ T	30
	DNA pilot	H	53	Q $\to$ K	4683	A $\to$ C	70
ID8evol2	Spike	G	2	F $\to$ L	3986	T $\to$ C	40
	DNA pilot	H	79	S $\to$ A	4761	T $\to$ G	80
	DNA pilot	H	336	S $\to$ F	5533	C $\to$ T	80
NC28wt1	DNA pilot	H	4	A $\to$ D	5098	C $\to$ A	10
	Scaffolding (lysis)	D/E	181 (59)	A $\to$ V (silent)	2871	C $\to$ T	30
	DNA pilot	H	230	T $\to$ A	5775	A $\to$ G	30
NC28wt2	DNA pilot	H	3	G $\to$ D	5095	G $\to$ A	10
	Coat	F	151	N $\to$ S	3537	A $\to$ G	40
	Coat	F	240	H $\to$ R	3804	A $\to$ G	40
	DNA pilot	H	265	G $\to$ A	5881	G $\to$ C	50
NC28evol1	Noncoding				389	G $\to$ T	10
	DNA pilot	H	230	T $\to$ A	5775	A $\to$ G	10
	DNA pilot	H	7	G $\to$ D	5107	G $\to$ A	30
	Spike	G	176	A $\to$ V	4933	C $\to$ T	60
NC28evol2	DNA pilot	H	6	V $\to$ L	5103	G $\to$ T	20
	DNA pilot	H	230	T $\to$ A	5775	A $\to$ G	30
	DNA replication	A	115	A $\to$ T	1101	G $\to$ A	60

A list of the mutations that fixed during the adaptation of the ID8 and NC28 wild-type and evol lineages, under selection on growth rate and capsid stability. Certain regions of the bacteriophage genome have overlapping genes, indicated with the second affected gene in parentheses. The final column lists the first passage in which the mutation was observed in whole-population Sanger sequencing performed every 10 passages. Aa, amino acid; Nuc., nucleotide; obs., observed.