13.4 Running lm_map with phenotypic data

./lm_map map_P.par

Running this example takes a noticeable amount of time. Given are the MLEs of the sex-averaged recombination frequency in each of the two marker intervals and of the mistyping (error) rate. Also given is the estimated variance-covariance matrix of these MLEs and the effective number of meioses (see the previous section).

MAXIMUM LIKELIHOOD ESTIMATES Interval Sex-Averaged (RF) -------- ---------------- 1 0.1510 2 0.1787 MISTYPING RATE: 1.479401% ESTIMATED VARIANCE OF (MAP,MISTYPING RATE) SEX-AVERAGED ------------------------------------------------------ 0.001432 -0.000482 0.000007 -0.000482 0.001517 -0.000016 0.000007 -0.000016 0.000072

Following this section, there is a table of the estimated error probability for each individual at each marker. From your output you should see that the program detects errors in individual 32 and individual 49 for marker-3 and in individual 90 for marker-1. Some other instances of data with low (non-error) probability also show non-zero estimated probability of error. The exact values of these probabilities will depend on the random seeds used in the run.