Table II. Mapping the sequence reads with different BLAT and BLAST parameters to empirically determine suitable mapping conditions.

The percentage of AGI codes with at least one mapped read and the average mappings per read were determined prior to parsing the tables to retain only the best match. Suitable mapping conditions are printed in bold; for BLAT, the cutoff value is the minimal number of matching bases; for BLAST, it is the minimal accepted e-value.

Mapping Program	Library	Search Space	Cutoff Value	Percentage Reads with at Least One Hit in the Reference	Percentage AGI Codes with at Least One Mapped Read	Average Mappings per Read
BLAT	C. gynandra	DNA	60	40.9	42.0	1.19
			75	40.7	41.7	1.19
			85	30.2	35.8	1.15
			90	7.7	19.5	1.09
		Protein	25	82.6	70.4	2.35
			50	82.6	70.4	2.35
			75	75.4	62.6	1.48
			80	56.4	52.2	1.27
	C. spinosa	DNA	60	40.8	38.9	1.29
			75	40.6	38.5	1.28
			85	29.7	32.3	1.21
			90	8.5	17.1	1.15
		Protein	25	83.0	67.7	2.49
			50	83.0	67.7	2.46
			75	76.0	58.9	1.57
			80	57.9	48.4	1.32
BLAST	C. gynandra	DNA	1e-05:	68.9	56.5	30.7
			1e-10:	58.8	49.1	27.7
			1e-30:	29.6	30.5	18.9
			1e-50:	9.9	15.9	11.5
		Protein	1e-05:	78.0	76.9	106.6
			1e-10:	67.8	71.0	64.6
			1e-30:	29.0	39.5	22.9
			1e-50:	0.1	0.3	7.5
	C. spinosa	DNA	1e-05:	69.7	53.0	28.2
			1e-10:	59.6	46.3	25.1
			1e-30:	29.4	28.3	16.2
			1e-50:	9.8	14.4	9.8
		Protein	1e-05:	78.8	75.3	93.7
			1e-10:	68.3	68.7	56.4
			1e-30:	29.3	36.0	21.2
			1e-50:	0.1	0.3	4.6