Fig. 8

gramtools mapping and coverage recording. a Variant-aware Burrows Wheeler Transform (vBWT). Each row of the text matrix encodes one position in a linear representation of the graph. BWT: stores the character in the previous position; SA: suffix array, stores the position in the text; suffix: stores the text from SA position to the end. Two markers are used for every variant site in the genome graph: odd markers mark site entry and even markers allow alleles to sort and be queried together. Black intervals mark regular BWT backward searching, with each match to the currently mapped base shown in green. Arrows from red intervals mark vBWT-specific jumps in and out of sites, making the search branch. The read being mapped is shown in dashed orange. b Square brackets under allele nodes show per-base coverage storage. Another array shown below stores allele-level coverage at each site. Mapped reads increment equivalence class counts representing compatibility: in this example, the read is compatible with both alleles 0 and 1 at site 5 and only with allele 1 at site 7. Both kinds of coverage are used in genotyping