Table 1.

Read counts mapped to representative genomes across time points

Time point (days)	Total read number	Mapped read number	% of reads mapped	Number of genomes detected*
0	55398280	40291503	72.73	92
82	62544544	43877427	70.15	82
166	60931806	46030350	75.54	103
284	56282006	48644523	86.43	68
328	127048582	95132145	74.88	87
437	119945232	93737087	78.15	60

^*Number of representative genomes based on threshold of > 1 coverage and > 0.5 breadth