Table 3.
Human bisulfite read experiment
| Evaluation metric | GNUMAP-bs | Novoalign | BSMAP | Bismark | Bismark-bt2 | LAST | BRAT-BW |
|---|---|---|---|---|---|---|---|
|
All chr22: |
|
|
|
|
|
|
|
| Reads Aligned |
1.57M |
1.65M |
1.34M |
1.31M |
1.21M |
3.02M |
0.98M |
| CGs Covered |
330K |
336K |
330K |
310K |
299K |
373K |
275K |
| CG read coverage |
6.3 |
6.1 |
5.8 |
5.8 |
5.7 |
7.6 |
5.0 |
|
HEP overlap: |
|
|
|
|
|
|
|
| CGs Covered |
7,902 |
7,802 |
7,747 |
7,561 |
7,331 |
8,606 |
6,690 |
| Correlation |
0.887 |
0.889 |
0.887 |
0.888 |
0.895 |
0.882 |
0.894 |
| Concordance |
0.869 |
0.867 |
0.865 |
0.867 |
0.872 |
0.858 |
0.872 |
| CG Read coverage | 4.6 | 4.5 | 4.4 | 4.3 | 4.3 | 4.9 | 3.7 |
Study of 162.3 M Illumina BSRs on human chromosome 22 (chr22) from a human donor sample. The top rows show the overall mapping efficiency, including covered CGs sites and read coverage aligned to chr22. The bottom rows show the consistency of each mapping result with known methylation levels at 13,563 CGs sites on chr22 available from the HEP database. The concordance statistic is defined as the fraction of overlapped CGs covered by the aligner with HEP CGs for which the methylation prediction error was smaller than 0.25.