Pyrosequencing has problems with determining the correct number of bases in a homopolymer stretch. However, we notice that this problem is much more frequent with polyA than polyT/C/G. How can that be?

I found a paper describing roughly the same thing (but with polyA/T), but without any explanation. Could it be that the fluorescent reporter used for dATP is weaker than for the other bases, making it more difficult to determine peak size? The problem starts already at a three base repeat, giving ~10-20% sequences with runs of lengths two, four, five and even six bases.

I found a paper describing roughly the same thing (but with polyA/T), but without any explanation. Could it be that the fluorescent reporter used for dATP is weaker than for the other bases, making it more difficult to determine peak size? The problem starts already at a three base repeat, giving ~10-20% sequences with runs of lengths two, four, five and even six bases.

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