SNP density plots of genome sequence reads from T. gondii clones compared against the ME49 reference genome. The top two panels represent the ME49 and VAND parental lines. The middle two panels represent two recombinant clones that show mixed genotypes that match ME49 vs. VAND in different regions. The bottom two panels show a ME49 self-clone and VAND self-clone. X-axis indicates the relative sizes of 14 chromosomes of T. gondii. Y-axis indicates the number of SNPs per kb using a 5 kb sliding window. Top row indicates the location of 8 genetic markers used to determine the recombinant clones. Unk indicates unlinked and unmapped sequences.