Analysis Output | Analysis Reports | Sample Reports | Alignment Summary

Alignment Summary

Table 11 Alignment Quality Table
Statistic	Definition
Total Aligned Reads (% Reads)	Percentage of reads passing filter that aligned to the reference.
Abundant Reads (% Reads)	Percentage of reads that aligns to abundant transcripts, such as mitochondrial and ribosomal sequences.
Unaligned Reads (% Reads)	Percentage of reads passing filter that are not aligned to the reference.
Reads with spliced alignment (% Aligned Reads)	Percentage of aligned reads with a spliced alignment.
Reads aligned at multiple loci (% Aligned Reads)	Percentage of aligned reads to multiple loci.

If a panel is selected, the app calculates the alignment information based on the on-target genes.

Table 12 Alignment Information Table
Statistics	Definition
Coding	Metrics based on coding bases.
UTR	Metrics based on bases in untranslated regions (UTR).
Intron	Metrics based on bases in introns.
Intergenic or Non-targeted	Metrics based on bases in intergenic or non-targeted regions. The app reports "non-targeted" if a panel is selected.