Read # Bacteria Genomes   A B C D 1 95 5 0 23 2 98 0 3 4 3 92 3 4 0 4 5 0 95 2 5 3 2 100 3 6 2 4 98 14 Genome A assigned reads: 1, 2, 3,... Genome C assigned reads: 1, 2, 3,...

Table 1: Notional figure showing filtered reads (#1-5) and assignment to genomes for hypothesis testing based percent of matching n-mers per read to n-mers in reference genomes (A, B, C, D). The n-mers matched in the genome need to be contiguous, as they are in the read.