Table 1.

Read depth and targeting efficiency from nanopore Cas9 targeted sequencing in FSHD1 and FSHD2 participants and healthy controls

Participant ID	Total Mapped Reads	All On-target Reads			4q On-target Reads			10q On-target Reads			D4Z4 On-target Reads (3.3kb)		Divergent D4Z4 Reads
		Total	% p13-pLAM	% D4Z4	p13	pLAM	Full Array	p13	pLAM	Full Array	4q	10q	Reads	% Total
Cas9 gRNA:p13E-11+pLAM a
P1	35,019	392	1.1%	-	91	78	68 (6U)	109	114	38 (11U) 34 (13U)	-	-	16,368	46.7%
P2	30,954	207	0.7%	-	64	70	39 (6U)	35	38	5 (13U)	-	-	17,631	57.0%
P3	116,981	613	0.5%	-	137	183	78 (6U)	143	150	36 (9U)	-	-	42,885	36.7%
P4	77,047	319	0.4%	-	83	107	50 (6U)	59	70	7 (13U) 1(19U)	-	-	23,604	30.6%
P5	18,256	179	1.0%	-	62	36	15 (9U-S) 10 (9U-L)	56	25	0	-	-	8,381	45.9%
P6	27,317	139	0.5%	-	48	54	36 (3U)	14	23	1 (13U)	-	-	9,044	33.1%
P7	53,538	385	0.7%	-	30	34	4 (19U)	171	150	63 (8U) 34 (12U)	-	-	13,583	25.4%
P8	52,066	254	0.5%	-	33	42	11 (16U) 1 (26U)	87	92	39 (10U) 1 (25U)	-	-	20,093	38.6%
Cas9 gRNA:p13E-11 a
P2	30,734	77	0.3%	-	27	0	0	50	0	0	-	-	42	0.1%
Cas9 gRNA:D4Z4 b
C1	9,042	2,741	-	30.3%	-	-	-	-	-	-	1,077	1,664	512	5.7%
C2	10,345	2,555	-	24.7%	-	-	-	-	-	-	1,424	1,131	321	3.1%
P9	6,431	410	-	6.4%	-	-	-	-	-	-	217	193	138	2.1%
P10	1,418	476	-	33.6%	-	-	-	-	-	-	258	218	66	4.7%
P1	6,977	826	-	11.8%	-	-	-	-	-	-	372	454	246	3.5%
P1	3,348	339	-	10.1%	-	-	-	-	-	-	162	177	117	3.5%
Cas9 gRNA:p13E-11+pLAM+D4Z4
P9a	116,799	3,582	0.5%	2.6%	115	210	40 (6U)	107	109	0	1,524	1,517	37,467	32.1%
P10a	39,605	1,979	0.7%	4.3%	63	91	42 (6U)	55	50	8 (13U)	888	832	16,052	40.5%
C3c	9,952	1,219	0.2%	12.0%	3	10	0	5	4	0	806	391	4,152	41.7%
Ultra -Long kit V14 d
C4	6,140,482	253	0.004%	0.037%	74	51	14 (16U) 4 (41U)	62	66	10 (20U) 5 (21U)	-	-	-	-

^aSequencing on MinION R9.4.1 flowcell;

^bSequencing on Flongle R9.4.1 flowcell;

^cSequencing on MinION R10.4.1 flowcell;

^dSequencing on PromethION 10.4.1 flowcell.