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 |