Table 1.

PMM Counts in Children across Different Allele Fraction and Coverage Thresholds

		syn	mis	non+splice	Total
Best Practice Filters
Quads	Pro	94	195	20	309
	Sib	62	203	15	280
Trios	Pro	26	63	6	95
	Total Pro	120	258	26	404
AF 5%-45× High Confidence
Quads	Pro	58	131	12	201
	Sib	42	133	10	185
Trios	Pro	22	53	6	81
	Total Pro	80	184	18	282
Total germlinea	Pro	246	704	73	1,023
	Sib	186	431	26	643
AF 15%-45× Burdenb
Quads	Pro	24	65	5	94
	Sib	20	66	5	91
Jointly covered bases: 24.5
Trios	Pro	8	30	0	38
	Total Pro	32	95	5	132
Jointly covered bases: 9.7
AF 12.5%-50× Burdenb
Quads	Pro	32	67	5	104
	Sib	16	80	6	102
Jointly covered bases: 22.3
Trios	Pro	12	31	2	45
	Total Pro	44	98	7	149
Jointly covered bases: 8.9
AF 10%-65× Burdenb
Quads	Pro	38	63	6	107
	Sib	20	76	4	100
Jointly covered bases: 16.7
Trios	Pro	12	31	1	44
	Total Pro	50	94	7	151
Jointly covered bases: 6.8
AF 7.5%-85× Burdenb
Quads	Pro	31	56	6	93
	Sib	18	66	5	89
Jointly covered bases: 11.4
Trios	Pro	11	28	4	43
	Total Pro	42	84	10	136
Jointly covered bases: 4.7
AF 5%-130× Burdenb
Quads	Pro	20	35	4	59
	Sib	12	35	2	49
Jointly covered bases: 5.1
Trios	Pro	10	18	5	33
	Total Pro	30	53	9	92
Jointly covered bases: 2.0

Abbreviations are as follows: AF, allele fraction; Pro, proband; Sib, sibling; syn, synonymous; mis, missense; non + splice, nonsense and canonical splicing. Bases in billions. Mutations with other annotations not shown.

^aGermline de novo mutations identified using our pipeline.

^bPMMs in sex chromosomes were excluded in this set.