Table 2.

Effect of reference genome choice

Species	Target value	Proportion without E. coligenome [%]	Proportion with E. coligenome [%]	Difference before [%]	Difference after [%]
Cattle	58.82	61.81	58.53	2.99	0.29
E.coli	5.89	0.00	5.86	5.89	0.02
Pig	11.76	13.00	11.74	1.24	0.02
Sheep	23.53	25.19	23.86	1.66	0.33

Simulation demonstrates the effect of choosing the adequate genomes for quantification by AFS. Initially, the E. coli reference genome was omitted in the mapping step. After observing E. coli reads in the metagenomic analysis, its genome was added to the mapping procedure, and the species proportions were now recovered with much higher accuracy.