Fig. 5: Characteristics of mega-NUMTs.

a Model showing the formation of mega-NUMTs and our strategy for their detection in whole genome sequence data. OH_, origins of heavy-strand replication; OL_, origins of light-strand replication. b Combined box and swarm plots show the estimated number of copies of the mtDNA-derived fragment within the NUMT in seven families. The middle “box” represents the median, lower and upper quartile of the data. The upper and lower whiskers represent the data outside the middle 50%. The dots represent the informative variants included in the mixed haplotype (Methods, Supplementary Table 4). c Modelling of the estimated variant allelic fraction for a NUMT at different true mtDNA sequencing depths. Modelling was based on whole genome nuclear sequencing (WGS) depths seen in our dataset (35×, 40×, 45× and 50×), and the corresponding variant fraction based on the number of copies of mtDNA-derived fragment within the NUMT. 95% confident intervals are shown for one copy and 20 copies. d Detected variant allelic fraction for each of the seven families related to the true mtDNA per-base sequence depth. Upper and lower symbols show the trend of variant allelic fraction estimated from WGS depth 50× with 20 copies of mtDNA-derived fragments and WGS depth 35× with 1 copy of mtDNA-derived fragment.