Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

Table 4. Distance thresholds and conversion values.

Method	Distance function	Distance threshold¹	Error-ratio	Intercept (c)	Slope (m)
NCBI BLAST	Trimming (1)	0.2676	0.0860	96.8979	−121.4848
	Trimming (2)	0.0412	0.0430	90.3998	−438.3134
	Trimming (3)	0.2945	0.0860	98.6313	−118.8770
WU-BLAST	Trimming (1)	0.0436	0.2796	122.9402	−406.2128
	Trimming (2)	0.0870	0.0430	82.1068	−166.2293
	Trimming (3)	0.2870	0.0860	115.4105	−191.9086
BLAT	Trimming (1)	0.2672	0.0753	97.7166	−127.9852
	Trimming (2)	0.0416	0.0430	87.0748	−376.3038
	Trimming (3)	0.2811	0.0645	100.6280	−122.5151
BLASTZ	Trimming (1)	0.2389	0.2043	89.8757	−102.0887
	Trimming (2)	0.0575	0.0538	85.1650	−273.1803
	Trimming (3)	0.3344	0.1828	111.9235	−125.1989
MUMmer	Coverage (1)	0.6110	0.0430	130.9618	−116.4258

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