For instance, if a sequence has a high GC content, expect to see more errors than suggested by the error rates above. These error rates are already out of date. With advent of Big Dye-terminators, error rates have decreased by a factor of about two and 'good' regions now extend to the 550bp mark and beyond. The only viable way to achieve these ends is by carrying out multiple sequencing runs, either in different directions or using different chemistries, or both. As far as systematic errors are concerned, it's also advantageous to do more than one-pass sequencing.
Compressions tend to occur at different places when sequencing in different directions.
Hence, at any particular position, at least one of the strands will be unlikely to be prone to compression effects. It is now unclear whether using two chemistries is really as good as sequencing in both directions. However, both remain a standard at this time. No matter how many times you sequence your DNA, you can tell the reliability of each of your called bases by looking at the quality assigned by Phred. Studies have shown that these quality scores are themselves reliable, see Figure 1.