Table 3.

Parameter evaluation using a 454-model using flowpeak information

Parameters/ID	40%	50%	60%	70%	80%	90%	100%
S = 30, D = 60, h = 0.2, k = 0.4, V = 1	0.681	0.682	0.708	0.748	0.775	0.796	0.815
S = 30, D = 60, h = 0.2, k = 0.5, V = 1	0.681	0.683	0.712	0.752	0.782	0.803	0.823
S = 20, D = 40, h = 0.3, k = 0.4, V = 1	0.673	0.677	0.706	0.757	0.788	0.812	0.833
S = 30, D = 60, h = 0.2, k = 0.8, V = 1	0.666	0.671	0.701	0.757	0.791	0.817	0.839
S = 15, D = 30, h = 0.4, k = 0.5, V = 1	0.613	0.629	0.673	0.744	0.782	0.825	0.849
S = 8, D = 15, h = 0.7, k = 0.4, V = 0	0.321	0.317	0.455	0.639	0.697	0.774	0.862

The table describes the Matthews Correlation Coefficient of the homopolymer insertion/deletion recovery for various parameter combinations using flowpeak information (i.e. SFF input). The results are evaluated using alignments against targets of a protein identity ranging from 40 to 100%, not including potential sequencing errors. The best results are highlighted in bold for each column as well as the parameter set which results in the best mean MCC (default parameters).