Supplementary Figures
Supplementary Figure 1 Basic overview of the long-read targeted
phasing approach . Red boxes highlighting failed sample outcomes.
Supplementary Figure 2 Long range PCR performance and
optimisation. (a) change standard to rapid. Percentage
comparison of first-time primer success using our standardised approach
and primer success after optimisations at increasing target sizes (kb).(b) Table of optimisation categories, displaying total target
amplification success rates at each stage.
Supplementary Figure 3 a) Log10 scatter plot of target
amplification sizes in relation to the percentage of false allele
coverage of each target and the percentage of false iSNP/DNM base
coverage of each target. The trend of the data is highlighted by the
logarithmic line of best fit. b) Log10 scatter plot of target
amplification sizes in relation to the percentage of bases with quality
score <5 (see method section ‘Bioinformatics’). The trend of
the data is highlighted by the logarithmic line of best fit.
Supplementary Figure 4 Violin plot comparing the WES DNM
nucleotide base frequencies, ONT DNM nucleotide base frequencies, ONT
DNM allele frequencies, ONT DNM prezygotic and postzygotic allele
frequencies.
Supplementary Figure 5 Pre and post zygotic illustrative
breakdown of the 77 DNMs that could be phased, including the parental
origin of the DNMs.
Supplementary Figure 6 Stacked percentage plot looking at
parent-of-origin in relation to likelihood of causality.
Supplementary Figure 7 IGV illustration of a DNM showing a
comparison of WES and ONT data. Using long-read targeted sequencing,
the ~1700 bp region that these variants span was
sequenced and visualized in IGV. Approximately 15000 reads are phased in
the ONT data, and the quality and coverage differences between those
reads and the WES reads can be observed.