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 ProgramLibrarySearch SpaceCutoff ValuePercentage Reads with at Least One Hit in the ReferencePercentage AGI Codes with at Least One Mapped ReadAverage Mappings per Read
BLATC. gynandraDNA6040.942.01.19
7540.741.71.19
8530.235.81.15
907.719.51.09
Protein2582.670.42.35
5082.670.42.35
7575.462.61.48
8056.452.21.27
C. spinosaDNA6040.838.91.29
7540.638.51.28
8529.732.31.21
908.517.11.15
Protein2583.067.72.49
5083.067.72.46
7576.058.91.57
8057.948.41.32
BLASTC. gynandraDNA1e-05:68.956.530.7
1e-10:58.849.127.7
1e-30:29.630.518.9
1e-50:9.915.911.5
Protein1e-05:78.076.9106.6
1e-10:67.871.064.6
1e-30:29.039.522.9
1e-50:0.10.37.5
C. spinosaDNA1e-05:69.753.028.2
1e-10:59.646.325.1
1e-30:29.428.316.2
1e-50:9.814.49.8
Protein1e-05:78.875.393.7
1e-10:68.368.756.4
1e-30:29.336.021.2
1e-50:0.10.34.6