On the Analysis of Optical Mapping Data - University of Wisconsin ...

34
250
200
0.700 − 0.005
0 50 100 150 200 250
0.750 − 0.005 0.800 − 0.005
150
100
50
Quantiles of GMO7535 fragment lengths
0
250
0.700 − 0.003 0.750 − 0.003
0.700 − 0.001 0.750 − 0.001
0.800 − 0.003
0.800 − 0.001
250
200
150
100
50
0
200
150
100
50
0
0 50 100 150 200 250
Quantiles of fragment lengths in simulated data
0 50 100 150 200 250
Figure 2.6 Diagnostic plots based on the distribution of observed optical map fragment
lengths. This is similar in principle to Figure 2.2, and in fact has the same quantities on
the vertical axis, namely the quantiles of observed fragment lengths of GM07535 optical
maps. However, instead of quantiles of exponential, the horizontal axis here has quantiles
of fragment lengths in optical map sets simulated using various combinations of parameter
values. The effect of desorption appears to have been modeled fairly well. The spurious
cut rate ζ appears to have little effect (at least for the values used here), but the digestion
probability p certainly does.