Fig. 3.

Example of errors in scaffold orientation. The top panels show the Hi-C contact matrix for barley chromosome 3H before (a) and after (b) manual correction. The bottom panels show the directionality biases in the Hi-C data as defined by Himmelbach et al. [47] before (c) and after (d) manual correction. Two inverted scaffolds are evident as deviations from the expected Rabl configuration [3] and as diagonals bounded by discontinuities in the directionality biases