This option in the Contig settings is designed to help separate out similar amplicons into different contigs. For optimal performance, contigs should consist of trace files amplified from the same primers.
Trace files of amplicons with a high degree of overlap may get grouped into the same contig under default settings. To prevent this, select “Exclude 1st Base Difference” from the Contig tab of the Mutation Project Settings and select a value for an appropriate distance between the amplicon starts.
Technical Example:
When unselected, the software uses 300 as starting point and sorts lanes with a starting base difference greater than 300 bases into two contigs
If a 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 the fat peaks at the end of the sequence in the reference are being compared with the front sharp peaks of the second sample. If this option is selected and set to 100, the software would sort the two samples into different contigs.