Fig. 4

Genomic tracks showing evidence for genotype calls from Strand-seq composite files (forward reads green, reverse reads orange) at HGSVC inversion coordinates (black bars; [3]). A This inversion is HET according to both InvertypeR and manual inspection but is REF according to the HGSVC. B InvertypeR called this ambiguous, the HGSVC called HET, and manual inspection shows this to be an alignment error or reference assembly collapse because the WC composite file (bottom) has no strand switch. The HGSVC [3] did not use a WC composite file and may have missed this. C Two adjacent HET inversions according to the HGSVC. InvertypeR returns an ambiguous call. Manual inspection indicates unclear strand-switches and likely alignment errors. D A guide to manual inspection. The second box in each triple represents the putative inversion, while the first and third represent flanking sequences. Putative inversions are likely false positives unless the strand states clearly match the patterns shown for HOM or HET. Note that the colour of the second box for deletions and HET inversions may be either solid orange or solid green (i.e., just not WC)