Table 2.

Exome sequencing quality and summary of rare homozygous and de novo variants

Trio	Coverage proband		Coverage mother		Coverage father		Rare homo	X-linked	Cpd hets	de novos		Variants of interest
	Captured regions with coverage >10 (%)	Average coverage captured regions	Captured regions with coverage >10 (%)	Average coverage captured regions	Captured regions with coverage >10 (%)	Average coverage captured regions				Confirmed by Sanger sequencing/TaqMan	Not confirmed but high coverage, good quality alignment
1	89.8	115	90.19	64	90.59	65	25	17	0	EFTUD2 i-e	ZPF90 NS, TMEM175 S	EFTUD2
2	88.9	63	87.5	60	88.37	58	6	9	2	none		NGLY1
3	88.2	58	85.2	48	86.29	45	9	6	0	SMAD4 NS	NTSR1 NS, AC121493.1 NS	SMAD4
4	91.5	80	88.34	72	90.85	73	15	NA	0		AT6AP2 NS	EFEMP1
5	90.1	64	90.67	71	91.02	67	7	NA	1	TCFA NS	RBM43 NS	TCFA
6	88.9	60	87.18	102	89.07	61	16	6	0	HNRNPU ESS	SMAD1, NS	HNRNPU, SMAD1
7	87.3	68	89.75	87	90.33	94	7	8	0	EFTUD2 FS		EFTUD2
8	85.9	55	89.72	81	92.39	106	3	4	0			None
9	89.3	57	80.68	100	85.63	60	36	NA	0		ZNF266 S, C12OR51 NS, SAMD13 FS	None
10	90.8	72	90.59	68	78.37	83	6	5	0		MAST1 NS
11	91.6	88	89.54	67	89.22	71	8	5	1	SCN2A NS	TBC1D1 NS	SCN2A
12	91.0	77	90.61	68	90.33	71	4	NA	0		NR1H3 NS, AP4M1 in	None

1=percentage of captured regions with coverage>5; 2=average coverage captured regions (x); NS, non-synonymous, S, synonymous; i-e, intron-exon boundary; in, intronic variant; FS, frameshift variant; ESS, change in essential splice site.