What is the function of Exclude 1st Base Difference in the Options window?
When unselected, the software uses 300 as starting point and sorts lanes with a starting base difference greater than 300 bases into two contigs. For example, the reference covers 1 — 700 bases, sample one covers 10 to 600 base, and the 2nd sample covers 500-900 bases, then the software would sort them into the same contig. However, it would be very difficult to find mutations, because of the fat peaks at the end of the sequences with which is compared to the front sharp peaks. If this option is selected to 100, the software would sorts the two samples into two contigs.
