Table 1. Sample overview.

Family	Sample	Sanger.Junc	PacBio.Junc	Duplication.Haplotype	Y-chr haplogroup
1	P1	1	1	1*/4	I
1	F1	1	1	1*/o	I
1	B1	1	1	1*/2	I
2	P2	1	1	1*/2	I
2	F2	1	1	1*/4	I
3	P3	1	1	1/2	I
3	F3		1	1/2	I
4	P4	1	1	3*/2	R
4	F4	1	1	3*/o	R
5	P5	2	2	2*/o	I
5	F5	2	2	2*/2	I
6	P6	1	1	2*/2	I
6	F6	1	1	2*/4	I
7	P7	1	1	1/2	I
8	P8	1	1	1/2	I
9	P9		1	1/1	I
10	P10		2	2/o	I
11	P11		1	1/2	I
12	P12		1c	failed	I
13	P13		1	1/2	I
14	P14	1	1	1/o	I
15	P15		1	2/o	I

If appropriate, each sample has indicated family and relationship: P -patient, B -brother, F -father, Sanger.Junc is the sequencing results of Figure 2 C. PacBio.Junc indicates the breakpoint haplotype deduced from the PacBio amplicons. 1c is the same as junction 1, with the addition of SNP rs211656. Duplication.Haplotype indicates the PacBio phased alleles from the duplicated region found in Figure 2 D (o  =  other haplotype). * indicates the deduced allele of paternal origin in father-son-(brother) pairings. Y-chr haplogroup is the main haplotype groups from chromosome Y SNP-based analyses (Figure S2).