TPR vs FDR curves for deletion and duplication predictions of CONGA.

• Main Authors: Arda Söylev (14259721), Sevim Seda Çokoglu (14259724), Dilek Koptekin (4591300), Can Alkan (9984), Mehmet Somel (133767)
• Format: Still Image
• Language: unknown
• Published: 2022
• Subjects: Genetics; Evolutionary Biology; Ecology; Cancer; Infectious Diseases; Virology; Biological Sciences not elsewhere classified; systematic cnv analyses; single nucleotide polymorphisms; sampling experiments suggest; nine different laboratories; copy number variants; technical challenges posed; ancient genome analyses; conga thus paves; ascertained deletions across; technical factors; genotyped deletions; genotype deletions; ancient shotgun; ancient genomes; xlink ">; used conga; snps ); sequenced genomes; read length; present conga; population origin; major contributor; largely confined; homozygous states; highly correlated; heterogenous set; genotype 10; evolutionary adaptation; effectively applied; coverages ranging; 121 bps; 1 kbps; 002 outgroup; 000 years; &# 8805; Saqqaq
• Online Access: https://doi.org/10.1371/journal.pcbi.1010788.g004

Here, we use Mota, Saqqaq and Yamnaya genomes down-sampled to various depths from their original coverages of 9.6×, 13.1× and 23.3×, respectively. The numbers inside boxes show the down-sampled coverage values. We calculated TPR and FDR for down-sampled genomes assuming that our CONGA-based predictions with the original genomes (full data) reflect the ground truth. These predictions, in turn, were made using modern-day CNVs as candidate CNV list. The purpose of the experiment was to evaluate accuracy at lower coverage relative to the full data, as well as to compare performance across different real genomes ( Methods ).