FIG 2 .

Heterozygous allele frequencies and read depths for selected chromosomes of two L. tropica isolates, K26 (India) and Ackerman (Israel). (A) K26 (chromosomes 23, 24, and 28); (B) Ackerman (chromosomes 9, 11, and 24). Variants called homozygous differences from the L590 reference scored either 1 or 0 and are depicted in the 0.1 or 0.9 y axis range. Variants called heterozygous show allele frequencies around 0.5 in the hybrid line for all disomic chromosomes. Variants called heterozygous on trisomic chromosomes show allele frequencies around 0.33 and 0.67 in the hybrid line. Allele frequency and the total number of biallelic SNPs are shown in the upper panel, and read depth across the chromosome is shown in the lower panel for each chromosome. Median read depth, marked by a red line, was approximately 50 reads for disomic chromosomes.