Fig. 5: Switch errors in antifreeze protein tandem arrays. | Heredity

Fig. 5: Switch errors in antifreeze protein tandem arrays.

From: Mitigating assembly and switch errors in phased genomes of polar fishes reveals haplotype diversity in copy number of antifreeze protein genes

Fig. 5

Realignments of HiFi reads back to the reference genome species for Pholis gunnellus (left) and simulated switch errors (right) are visualized in IGV (top row) and input to the switch_error_screen tool, which calculates the risk of a switch error according to soft clipping (bottom row). An artificial switch error was introduced to the ancestral antifreeze protein array in the P. gunnellus reference genome for the purpose of comparison to an unaltered P. gunnellus array with low switch error risk. Soft clipped bases are colored in the IGV visualizations. Ranges of AFP gene annotations are visualized on the bottoms of IGV images as dark blue rectangles. A blue highlight in the left switch error index plot denotes the range of AFP tandem arrays in the ancestral locus.

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