Megabase-scale methylation phasing using nanopore long reads and NanoMethPhase

Table 1 Different metrics for SNV calls using Clair and Clair + SNVoter

Tool	Sample	QT	All TP	TP	FP	Acc	Pre	Rec	F1
C	Colo829BL	725	3,638,416	2,664,923	774,123	0.88	0.77	0.79	0.78
C+S	Colo829BL	160	3,638,416	2,851,683	336,594	0.93	0.89	0.84	0.87
C	NA19240 Run0	755	3,973,249	2,997,917	1,462,313	0.86	0.67	0.81	0.74
C+S	NA19240 Run0	170	3,973,249	3,160,297	956,846	0.90	0.77	0.86	0.81
C	NA19240 Run1	780	3,973,249	3,465,350	990,793	0.84	0.78	0.92	0.84
C+S	NA19240 Run1	350	3,973,249	3,436,275	658,067	0.88	0.84	0.91	0.87
C	NA19240 runs 1&2	800	3,973,249	3,644,703	812,335	0.84	0.82	0.96	0.88
C+S	NA19240 runs 1&2	180	3,973,249	3,595,674	683,727	0.86	0.84	0.94	0.89
C	NA19240 runs 0&1	820	3,973,249	3,639,922	750,137	0.85	0.83	0.95	0.89
C+S	NA19240 runs 0&1	170	3,973,249	3,592,467	653,594	0.85	0.85	0.94	0.89

C Clair, S SNVoter, QT quality threshold, TP true positive, FP false positive, Acc accuracy, Pre precision, Rec recall. All TP refers to all high-quality SNVs from 1KGP for NA19240 and from Strelka for Colo829BL Illumina sequencing

ISSN: 1474-760X