Skip to main content
. 2014 Jan 16;10(1):e1004092. doi: 10.1371/journal.pgen.1004092

Figure 5. Changes in SNP coverage depth pinpoint recombination breakpoints.

Figure 5

Chromosome 4 is trisomic in three of the strains, so changes in read depth for derived (non JPCM5-reference) alleles (A) show changes within some otherwise unphased blocks of heterozygous SNPs (B), showing recombination breakpoints not visible from simple plots of variant calls and not identifiable by other summary statistics (C). (A) shows derived allele read depth for the three trisomic strains, where changes in read depth inside the shaded boxes indicate presumed recombination events, where allele calls change from being present in 1/3 or 2/3 homologous chromosome copies. (B) Single-nucleotide polymorphisms (SNPs) with respect to L. infantum JCPM5 in a section of chromosome 4 across the 12 strains. Orange ‘blocked’ bars indicate heterozygous positions; green, red, blue and black indicate homozygous variant calls of A, C, G and T respectively. (C) Summary statistics for variant calls in 5 kb windows.