Table 1. Benchmark results of 14 pseudogenes cases described in literature.

Gene symbol	Publications	Agree	Precision	Artifacts highlighted	Comments
2310042E22Rik	[26], [27]	no	/	/	The gene was saved and detected as intact.
Gulo	[5], [26], [27]	yes	–	**	Problem of sensibility, tracks of pseudogenes are not detected
Acyl3	[26], [27]	yes	+	/	/
Uox	[6], [26], [27], [45]	yes	=	/	/
Ctf2	[26], [27], [46]	yes	+	/	/
Nradd	[26], [27], [47]	yes	+	*	/
Nepn	[26], [27], [47]	yes	+	*	/
Mup4	[27], [48]	yes	+	*	/
T2r2	[49]	yes	+	/	Pseudogene was described as polymorphic
Tas2R134	[27], [49]	yes	=	/	Tas2R134 and Tas2R143 Mus genes are co-orthologs to human pseudogene
1110012D08Rik	[27]	yes	+	*	/
Gpr33	[26], [27], [47]	yes	+	/	/
Slc7a15	[26], [27], [47]	yes	+	***	Some mutations are not seen due to artifacts
Sult3a1	[42]	yes	–	**	Artifacts leads to a scan in false frame, but the pseudogenization was confirmed manually

The Publications column indicates references of studies of the literature used as reference for comparison with GLADX results.

The Agree column contains yes if the case is consistent with the literature results and no when the result is in contradiction.

The Precision column indicates the quality of results obtained: “-” means low precision, “+” means a better precision, “ = ” means we found exactly the same results, and “/” means it can't be interpreted.

The Artifacts highlighted column indicates cases where artifacts are present: “*” are cases where GLADX found artifacts in databases (Text S2); “**” means artifacts caused by tools implemented in GLADX, and “/” means no artifact was observed.

The Comments column indicates some particularities, “/” means no particular comment.