text: user6483: Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a probabilistic model (a distribution) parameters (shape) of which will strongly depend on the details of the PCR protocol and the characteristics of the amplicon...
  If not, then may be there are forward models that predict the amount of the amplified result from the initial content?
  
  user6487: The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency).  NCBI 
  In this  article  on research gate they said  amplifx  was the software you were looking for to, calculate "(i.e. expected efficiency in PCR reaction)". The amplifx even mentions "Testing primers in in silico PCR".  
  
original_text: 6483: <p>Let's say I've run the PCR and I now have a certain amount of the amplicon product. Is there any model that infers how much of it was there before the PCR started? I suspect it should be a probabilistic model (a distribution) parameters (shape) of which will strongly depend on the details of the PCR protocol and the characteristics of the amplicon...</p>
  
  <p>If not, then may be there are forward models that predict the amount of the amplified result from the initial content?</p>
   6487: <p>The basic equation for PCR kinetics (Equation 1) states that the amount of amplicon after c cycles (Nc) is the starting concentration of the amplicon (N0) times the amplification efficiency (E) to the power c. The PCR efficiency in this equation is a number between 1 and 2 (2 indicates 100% efficiency). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2665230/" rel="nofollow noreferrer" > NCBI </a></p>
  
  <p>In this <a href="https://www.researchgate.net/post/How_can_I_calculate_the_expected_size_for_amplification_pcr_product_in_a_pcr_reaction" rel="nofollow noreferrer" > article </a> on research gate they said <a href="https://inp.univ-amu.fr/en/amplifx-manage-test-and-design-your-primers-for-pcr" rel="nofollow noreferrer" > amplifx </a> was the software you were looking for to, calculate "(i.e. expected efficiency in PCR reaction)". The amplifx even mentions "Testing primers in in silico PCR".  </p>
  