HMM Parameter Values.

The initial and trained values for the HMM. The first two columns (“1→2” and “2→1”) show the probability of transitioning from State 1 to State 2 and the reverse. The probability of transitioning from State 2 to State 1 is fixed at 0 (indicating a 100% probability of remaining in State 2). For each state, the probability of a match at each quality bin is reported. The initial values were used to validate the HMM. HMMSplicer uses Initial Value Set 2, though the initial values do not impact the final trained values (see Figure 2b). The trained values are shown for each dataset analyzed. The Human values are the same as those shown in Figure 1, though in more detail.