Table 1.

The number of fusion genes and breakpoints called in the non-cancer cell line NA12878 from ONT direct RNA and amplified cDNA. Most calls are presumed to be false positives. The number of fusions in the highest rank category for each tool is shown in bold. We hypothesize that most of the multi-read fusions reported by LongGF applied to the cDNA dataset (173) are chimeras introduced during library preparation. JAFFAL ranks these events as Low Confidence. The number of breakpoints for LongGF is not shown as it only reports one breakpoint per fusion gene by default

		Direct RNA			cDNA
Total reads processed		14,971,421			25,418,307
		Fusion genes	Break points	Reads support: median (range)	Fusion genes	Break points	Reads support: median (range)
Fusion genes called by JAFFAL	High confidence	4	4	4.5 (2–14)	8	8	6 (2–24)
	Low confidence	5	7	2 (2–11)	94	121	2 (2–49)
	Potential trans-splicing	344	344	1 (1–1)	412	412	1 (1–1)
Fusion genes called by longGF	>  1 Read support	5		2 (2–14)	173		2 (2–522)
	= 1 Read support	713		1 (1–1)	386		1 (1–1)