Table 7 Agreement among aligners in S1 trimmed data
Comparison pair | Class 1 | Class 2 | Class 3 | Class 4 | |
|---|---|---|---|---|---|
Randomly report one alignment per read | SOAP2 vs. Bowtie1 (6,409,534)2 | 95.89% | 3.95% | 0.13% | 0.03% |
SOAP2 vs.BWA (6,440,873) | 95.42% | 3.92% | 0.13% | 0.52% | |
Bowtie vs. BWA (6,432,433) | 95.30% | 4.21% | 0.00002% | 0.49% | |
SOAP2 vs. Novoalign (6,430,033) | 94.62% | 4.84% | 0.13% | 0.35% | |
Bowtie vs. Novoalign (6,422,084) | 94.77% | 4.84% | 0.07% | 0.33% | |
BWA vs. Novoalign (6,435,917) | 94.83% | 4.84% | 0.30% | 0.05% | |
Suppress reads with multiple alignments | SOAP2 vs. Bowtie (6,020,802) | 95.29% | 0.0002% | 4.68% | 0.003% |
SOAP2 vs.BWA (6,068,512) | 96.26% | 0.0005% | 2.93% | 0.81% | |
Bowtie vs. BWA (5,890,868) | 97.42% | 0.00% | 0.0004% | 2.58% | |
SOAP2 vs. Novoalign (6,043,150) | 98.47% | 0.95% | 0.18% | 0.40% | |
Bowtie vs. Novoalign (6,035,510) | 94.11% | 0.92% | 0.06% | 4.92% | |
BWA vs. Novoalign (6,066,586) | 95.62% | 0.92% | 0.57% | 2.90% |