Table 2 Target coverage statistics, median (interquartile range). Medians with different letters were significantly different (Tukey P < 0.05). All models included sample type as a random effect

Metagenome

0.63 (0.27–0.98)^ab

0.91 (0.81–0.98)^abc

0.987 (0.968–0.996)^abc

Metagenome-UMI

0.57 (0.22–0.98)^ab

0.90 (0.78–0.98)^abc

0.985 (0.962–0.996)^abc

Resistome

0.76 (0.32–0.99)^cd

0.91 (0.81–0.96)^abc

0.984 (0.966–0.992)^abc

Resistome-UMI

0.83 (0.34–1.00)^cd

0.94 (0.83–0.97)^d

0.989 (0.971–1.000)^d

Coefficients for sample type random effects

Beef 0.66

Poultry 0.76

Swine 0.75

WWTP 0.59

Beef 0.89

Poultry 0.91

Swine 0.91

WWTP 0.87

Beef 0.979

Poultry 0.983

Swine 0.983

WWTP 0.975