Transition matrix between chromatin states.
The first line is the probability of each chromatin state. The matrix below the first line is the Markov transition matrix between states (see Materials and Methods for its estimation). A value at the row and the column is the probability to find the chromatin state j in a 100 kb window next to a 100 kb window of chromatin state i. D corresponds to 100 kb windows that are not classified in any chromatin state.