. 2016 Feb 22;11(2):e0149426. doi: 10.1371/journal.pone.0149426

Table 3. Variant presenting coverage and variant frequency discrepancies between SeqNext and MiSeq Reporter.

	MiSeq Reporter						SeqNext						Comparison
	R1 WT	R1 mut.	R2 WT	R2 mut.	Cov.	VAF	R1 WT	R1 mut.	R2 WT	R2 mut.	Cov.	VAF	COV_SN/MR	VAF _SN/MR
c.1000C>T¹	276	53	71	52	452	23.2	70	53	70	52	245	42.9	0.54	1.85
c.1235del	210	136	213	207	766	44.8	217	216	220	219	872	49.9	1.14	1.14
c.2583del ¹	481	439	551	1	1472	29.9	550	373	0	0	923	40.4	0.63	1.35
c.2589_2599del ¹	220	156	61	0	437	35.7	225	155	0	0	380	40.8	0.87	1.14

Number of mutant (mut.) and WT reads in each direction, total coverage (Cov.) and VAF for variants presenting discrepancies between the two analysis pipelines using different primer trimming settings. Read count values showing discrepancies are in bold.

¹Variant located at a primer hybridization site.