Table 8 Agreement among aligners in S2 trimmed data
Comparison pair | Class 1 | Class 2 | Class 3 | Class 4 | |
|---|---|---|---|---|---|
Randomly report one alignment per read | SOAP2 vs. Bowtie1 (3,890,070)2 | 94.94% | 4.84% | 0.20% | 0.02% |
SOAP2 vs.BWA (3,900,529) | 94.69% | 4.82% | 0.20% | 0.29% | |
Bowtie vs. BWA (3,892,602) | 94.77% | 4.96% | 0.0002% | 0.27% | |
SOAP2 vs. Novoalign (3,909,055) | 93.84% | 5.32% | 0.34% | 0.50% | |
Bowtie vs. Novoalign (3,901,709) | 94.50% | 5.30% | 0.15% | 0.50% | |
BWA vs. Novoalign (3,908,656) | 93.96% | 5.30% | 0.33% | 0.41% | |
Suppress reads with multiple alignments | SOAP2 vs. Bowtie (3,611,489) | 96.20% | 0.0002% | 3.79% | 0.02% |
SOAP2 vs.BWA (3,636,423) | 96.42% | 0.0007% | 2.87% | 0.70% | |
Bowtie vs. BWA (3,531,986) | 98.38% | 0.00% | 0.0007% | 1.62% | |
SOAP2 vs. Novoalign (3,638,616) | 98.07% | 0.54% | 0.32% | 0.76% | |
Bowtie vs. Novoalign(3,631,179) | 95.06% | 0.52% | 0.11% | 4.31% | |
BWA vs. Novoalign (3,652,782) | 97.99% | 0.54% | 0.70% | 3.31% |