Table 5 Agreement among aligners in S1 non-trimmed data
Comparison pair | Class 1 | Class 2 | Class 3 | Class 4 | |
|---|---|---|---|---|---|
Randomly report one alignment per read | SOAP2 vs. Bowtie1 (5,626,038)2 | 96.25% | 3.41% | 0.34% | 0.002% |
SOAP2 vs.BWA (5,656,559) | 95.72% | 3.40% | 0.34% | 0.54% | |
Bowtie vs. BWA (5,637,504) | 95.80% | 3.66% | 0.00002% | 0.54% | |
SOAP2 vs. Novoalign (5,757,260) | 85.13% | 7.32% | 5.27% | 2.28% | |
Bowtie vs. Novoalign (5,748,724) | 85.18% | 7.26% | 5.13% | 2.47% | |
BWA vs. Novoalign (5,835,451) | 85.20% | 7.24% | 5.37% | 2.19% | |
Suppress reads with multiple alignments | SOAP2 vs. Bowtie (5,321,512) | 95.78% | 0.00002% | 4.22% | 0.003% |
SOAP2 vs.BWA (5,361,466) | 96.50% | 0.0005% | 2.75% | 0.75% | |
Bowtie vs. BWA (5,213,871) | 97.76% | 0.00% | 0.0004% | 2.24% | |
SOAP2 vs. Novoalign (5,447,206) | 88.14% | 4.27% | 5.28% | 2.31% | |
Bowtie vs. Novoalign (5,432,410) | 84.72% | 4.08% | 5.02% | 6.18% | |
BWA vs. Novoalign (5,458,788) | 85.92% | 4.11% | 5.48% | 4.49% |