IGV visualization of two high scoring (i.e., high likelihood) deletions and duplications predicted by CONGA.

The events displayed in the upper panels were detected in a modern-day human genome (NA07051: an ∼8 kbp deletion within chr7:16,169,440-16,177,556 and a ∼4 kbp duplication within chr7:22,496-26,553) and those in the lower panels in an ancient genome (RISE98: an ∼17 kbp deletion within chr6:32,506,809-32,524,264 and a ∼6 kbp duplication within chr1:1,520,604-1,526,959). The candidate CNV list used for genotyping was the long read CNV dataset described in Methods. Deducing the CNVs is straightforward with the modern-day genome data, however, it is less straightforward to distinguish these variations in ancient read data, especially for duplications. Note that this is one of the sample scenarios and we emphasize that a large number of CNVs identified in ancient genomes suffer from the same issue. (TIF)