If you have LOH detection enabled the Loss-of-heterozygosity track will contain detailed state predictions for both targets and variants by the hidden Markov model.
- The type of observation, i.e. coverage or variant.
- The most probable state, the following columns will contain the probabilities for each state.
- The columns starting with ``emission'' contain the probability of the observation given the state.
Since the model imposes a penalty on state changes this is not equal to the state probability, since this is influenced by nearby observations as well.