Fig. 1

Tracy web applications. The upper panel shows the trace viewer employed by Teal and Sage. The top toolbar of the viewer provides multiple buttons to scroll along the trace, zoom and highlight the trace signals for A, C, G and T. Sage augments the basic trace viewer of Teal by the reference alignment that highlights mismatches and gaps with respect to the reference sequence. The upper panel shows a trace alignment to the region chr11:108,202,140-108,202,185 with a 4bp deletion (red) and several single-nucleotide variants with double-peaks in the trace (yellow). The middle panel (Indigo) shows the allelic decomposition of a heterozygous 7bp deletion, the textual alignment of both alleles and a subset of the called variants. The trace aligned to the reference in reverse-complement orientation but the variants are reported based on the forward strand to comply with the VCF specification. The decomposition plot shows two minima, one allele (Alt1) has no insertion or deletion (local minimum at 0bp) and the other allele (Alt2) has a 7bp deletion (local minimum at -7bp). The variant table lists all called variants with respect to the reference, their genotype and the original basecalling and signal position in the trace, which are connected via hyperlinks to the trace viewer (not shown). The lower panel (Pearl) shows the reference sequence covered by traces (green) with mismatches highlighted in red. Below is the user interface of how to patch these reference mismatches for a selected position (3963, bold and red T) with the local trace information surrounding the T mismatch. The primary basecall at this position is a C, the secondary basecall a T. The buttons in the top toolbar can be used to edit the reference sequence based on the provided trace information. Conveniently, one can directly jump from one conflict position to the next without having to scroll through all traces