Table 1. Sample (artificial) variant data

POS	ID	REF	ALT	s1	s2	s3	s4	s5
1	a	T	TAA	0	0	1	1	0
4	b	TGG	AAAAAA	1	1	0	0	1
5	c	G	CC	0	0	1	1	0
12	d	AGTTA	T	0	0	0	1	1
16	e	AC	T, A	0	1	2	0	0

Note: The reference sequence is ‘TTCTGGGAGGCAGTTACC’. The last four columns encode the single chromosome copies for each sample.