Table 1.

Characteristics of VAFs before and after ABRA2 for Deletions

Case	Gene	Size of deletion	Estimated tumor cellularity, %	% Mismaps	% Mismaps fixed by ABRA2	VC VAF, %	Manual calculation of			Absolute difference between
							(1) Before ABRA2 VAF, %	(2) After ABRA2 VAF, %	(3) True NGS VAF, %	Before and after ABRA2 VAF (2) – (1), %	After ABRA2 VAF and true NGS VAF (3) – (2), %	Before ABRA2 VAF and true NGS VAF (3) – (1), %
1	CDKN2A	2	30	7.0	100	12.7	12.7	13.7	13.7	1.0	0	1.0
	TSC2	3		10.7	100	41.4	41.4	46.4	46.4	5.0	0	5.0
2	EGFR	18	20	38.0	88.9	12.0	11.9	18.3	19.1	6.4	0.8	7.2
	FOXO3	6		13.7	50	27.2	27.2	29.4	31.6	2.2	2.2	4.4
3	PIK3R1	6	30	21.7	97.7	29.6	29.6	37.6	37.7	8.0	0.1	8.1
4	CHD2	3	95	14.0	68.4	51.1	51.1	56.8	59.4	5.7	2.6	8.3
5	NF2	5	60	16.4	66.7	28.6	28.2	31.9	33.7	3.7	1.8	5.5
6	APC	8	60	23.2	63.2	21.9	21.9	26.0	28.5	4.1	2.5	6.6
	ARID1A	3		13.0	83.3	14.4	16.7	18.8	19.2	2.1	0.4	2.5
7	APC	1	60	5.0	100	65.5	65.4	68.9	68.9	3.5	0	3.5
	FANCD2	6		29.1	96.7	16.2	16.2	22.6	22.8	6.4	0.2	6.6
	PIK3R1	12		31.0	100	20.7	20.7	30.0	30.0	9.3	0	9.3
8	PRKDC	1	60	3.3	90.9	38.2	38.2	39.4	39.5	1.2	0.1	1.3
9	HIST1H2AM	2	80	6.6	96.8	42.5	42.5	45.4	45.5	2.9	0.1	3.0
10	APC	2	50	12.1	95	51.1	50.9	57.5	57.9	6.6	0.4	7.0
11	ATRX	1	90	5.0	100	37.7	37.7	39.7	39.7	2.0	0	2.0
12	JARID2	18	70	39.8	100	27.0	27.0	44.8	44.8	17.8	0	17.8
13	APC	13	40	31.1	97.9	15.8	15.8	22.8	23.0	7.0	0.2	7.2
45	KMT2D	30	100	72.4	97.7	16.6	16.5	58.8	59.8	42.3	1.0	43.3

VC VAF % calculated by the VC before the use of ABRA2; (1), (2), and (3): manually calculated by visualizing reads in Integrative Genomics Viewer.

ABRA2, Assembly-Based ReAligner; NGS, next-generation sequencing; VAF, variant allele frequency; VC, variant caller.