Table 2. Read alignment quality metrics for the NA12878 mapping experiment.

A total of 2% of NA12878 Illumina Platinum reads were mapped against the NovoGraph-constructed genome graph (“Genome graph”) and against a GRCh38-equivalent genome graph (“Reference graph”; no ALT contigs used). As expected, mapping against the genome graph increases mean alignment scores and alignment identities, albeit at a small reduction in the number of mapped reads.

	Genome graph	Reference graph
Mean scores	108.859	108.100
Mean identity value	0.9913	0.9891
Total mapped reads	31125004	31138410