TABLE 1.
Definitions of variables used for estimating mutation rates
| Symbol(s) | Definition |
|---|---|
| μs/n/c | Mutation rate as substitutions per nucleotide per cell infectiona |
| μs/n/r | Mutation rate as substitutions per nucleotide per strand copyinga |
| f, fs | Observed mutation frequency and observed mutation frequency for substitutions only, respectivelya |
| T, Ts | Total no. of mutations observable with a given detection method (mutational target size); subscript s is used to refer to substitutions onlya |
| L | Length (in nucleotides) of the genetic region studied |
| c | No. of cell infection cycles |
| B | No. of viral progeny particles released per infected cell (burst size, or viral yield) |
| N0 | No. of viral particles that start an infection (inoculum size) |
| N1 | No. of viral particles after growth |
| a | Exponential growth rate |
| W | Relative fitness as determined from growth rates and/or burst sizes |
| s | Fitness effect of a mutation, defined as 1 − W |
| E(sv) | Average s value of single random nucleotide substitutions, excluding lethal ones |
| pL | Probability that a single random nucleotide substitution is lethal |
| α | Selection correction factor |
| P0 | Fraction of cultures showing no mutants in the Luria-Delbrück fluctuation test (null class) |
| m | Mutation rate to a given phenotype per strand copying obtained from the Luria-Delbrück fluctuation testa |
| r, rc | No. of cycles of copying and no. of cycles of copying per cell infection, respectively |
| δ | Ratio of indels to total mutations (indel fraction) |
a
A subscript i is used analogously to refer to indels.