Fig. 2

Pangenome graph reference characterisation. A Example section of the graph for chromosome 1 showing different paths through the graph via segments originating from the 4 types of assemblies used to build the graph. B Total length of segments contained into the graph by type of assembly. Dashed areas represent the proportion of bases for segments covered by at least 2 samples with at least 5% of the average coverage over the HdrR reference segments. C Distribution of the length of segment by type of assembly normalised by the total length of segments. D Kernel density plots of the length of alternative segments according to their divergence when aligned onto the HdrR reference. The quadrants defined by vertical dashed lines (length = 2kb) and horizontal dashed lines (divergence = 0.5) separate the segments into 4 categories according to their length and divergence score. The numbers displayed correspond to the percentages of segments within each of the 4 quadrants. E Percentages of bases from nanopore reads aligning on each type of assembly for the 12 MIKK samples. F Detailed percentages of bases aligned on alternative segments for each MIKK sample depending on segments cross-usage by the other samples, from 12 (all other samples) to 1 (only the current sample). A segment was considered used by a sample when its coverage was at least 5% of the average HdrR reference coverage