Optimal reference sequence selection for genome assembly using minimum description length principle

EURASIP Journal on Bioinformatics and Systems Biology

Table 4 Variable number of insertions: the experiment shows the effect of increasing the number of insertions on choice of the reference sequence

Ref. Seq.	SNPs	No. of inversions	No. of insertions	No. of deletions	Code-length using proposed scheme (Kb)
1	0	0	136 / 196	0	1200.3
2	0	0	132 / 203	0	1228.25

The location and length of these insertions was chosen randomly. $\frac{136}{196}$ shows that out of 196 insertions in S_{R 1} only 136 were removed. The remaining insertions were not recovered due to the choice of τ₁ and τ₂. S_{R 2} has higher number of insertions as opposed to S_{R 1}. The code-length suggests that S_{R 1}is the model of choice as it has a smaller code-length.