The values for the average coverage for patient 4 and 5 are the total over the 2 runs (standard and titanium).
De novo assembly with Newbler yielded 354 contigs arranged in 14 scaffolds for SDD (NADC Z-8) and 9 scaffolds comprising 195 contigs for SDE1 (D166B) for an average coverage of 56.1 and 56.5, respectively.
The final assembly contained also contiguous sequences (>2× coverage/nt) on both strands for an average coverage of 5.5×; ambiguous bases were re-sequenced at least twice.
The 10 Kabuki cases were sequenced using an exome-capture kit for an average coverage of 40x on the mappable, targeted exome [ 8].
tissue, replicate, tissue.replicate and exon number.tissue were fitted as a fixed effect to correct for different average coverage per sample (and three samples per replicate).
A total of 349 regions, mainly coding exons along with 100 nucleotides of flanking sequences, were covered by >9,400 custom oligonucleotide probes for an average coverage of 27 probes per region.
Quality filtering of assembly contigs for size and average coverage resulted in 43,057 113,302 (mean = 76,390) contigs.
Inconsistent detection of exons is most pronounced for exons with average coverage of less than 5 reads per nucleotide.
For P. zelicaon, average coverage in the top 1% of β t was 10.64×, and the average β t in the top 1% of coverage was 1.29 × 10-3.
Instead, we consider a relative measure of nucleotide diversity β t developed by Novaes et al. [ 12], defined for contigs with average coverage at least 2×.
