Table 1.

A summary of the correspondence between HC1360, CC, PPC, and LIN-SL

Reference: query	Category	Count	Representative CCs
HC1360: CC	Consistent	344
	Incompatible	468	CC17 (n = 45); CC23 (n = 19); CC63 (n = 19); CC26 (n = 15); CC25 (n = 12); CC132 (n = 11); CC35 (n = 11); CC134 (n = 11); CC200 (n = 10); CC14 (n = 10)
	Merge	74
	Split	72
LIN-SL: CC	Consistent	386
	Incompatible	392	CC17 (n = 44); CC23 (n = 19); CC63 (n = 18); CC26 (n = 14); CC25 (n = 12); CC14 (n = 11); CC200 (n = 11); CC35 (n = 10)
	Merge	40
	Split	135
LIN-SL: HC1360	Consistent	599
	Incompatible	0
	Merge	0
	Split	242
LIN-SL: PPC	Consistent	648
	Incompatible	25
	Merge	31
	Split	157
PPC: HC1360	Consistent	632
	Incompatible	30
	Merge	52
	Split	127

^*consistent—identical clusters (comprise the same set of genomes); merge—multiple query clusters are merged into one cluster in the reference scheme; split—one query cluster is split into multiple clusters in the reference; incompatible—scenarios that cannot be assigned into any of the three categories above