Table 1.

Mixed effects models predicting the levels of six different measures of instability using age, the number of SBS2 and SBS13 mutations, accounting for the effects of tumour type as a random variable. The number of SBS2 and SBS13 mutations was log transformed using the natural logarithm. These models correspond to models 3-9, detailed in Additional file 1: Supplementary Note 1. SV structural variant, CN copy number, PGA Proportion of the Genome Altered, INDELs Insertions and Deletions, ID8 INDEL signature 8, ID6 INDEL signature 6, LMM linear mixed effects model, NB negative binomial, ZINB zero inflated negative binomial, AIC Akaike Information Criterion)

	Dependent variable:
		PGA	CN Segments	SVs	INDELs	ID8	ID6
	Model Type	LMM	NB	NB	NB	ZINB	ZINB
Count model: (Intercept)	Coefficient	3.62	4.42	0.397	1.36	0.514	5.46
	95% CI	(−9.49,16.7)	(4.01,4.83)	(−1.26,2.05)	(0.257,2.46)	(−1.52,2.55)	(1.30,9.63)
	p value	0.589	3.62x10−99∗∗∗	0.638	0.0157∗	0.620	0.0102∗
Count model: Age	Coefficient	0.0634	−0.000362	0.0323	0.0393	0.0250	−0.0562
	95% CI	(−0.0731,0.200)	(−0.00370,0.00298)	(0.00624,0.0583)	(0.0219,0.0567)	(−0.00703,0.0570)	(−0.121,0.0083)
	p value	0.363	0.832	0.0151∗	9.61x10−6∗∗∗	0.126	0.0877
Count model:	Coefficient	6.50	0.247	0.684	0.725	0.589	0.0191
log (SBS2/13)	95% CI	(4.99,8.01)	(0.206,0.289)	(0.442,0.927)	(0.562,0.888)	(0.281,0.897)	(−0.578,0.616)
	p value	2.51×10−16∗∗∗	5.66×10−32∗∗∗	3.14×10−8∗∗∗	3.43×10−18∗∗∗	1.77×10−4∗∗∗	0.950
Count model:	Coefficient			−0.00515	−0.00552	−0.00372	0.00738
Age:log (SBS2/13)	95% CI			(-0.00904,-0.00126)	(−0.00812,−0.00292)	(−0.00854,0.00110)	(−0.0019,0.0166)
	p value			0.00942∗∗	3.14×10−5∗∗∗	0.130	0.118
Zero model: (Intercept)	Coefficient					−0.684	1.07
	95% CI					(−0.839,−0.530)	(0.903,1.24)
	p value					4.20×10−18∗∗∗	3.85×10−36∗∗∗
AIC		6738.4	10,064.1	8701.2	10,444.3	6357.3	3270.9
Log likelihood		−3364.2	−5027.1	−4344.6	−5216.1	−3171.6	−1628.5
Num. obs.		725	725	717	725	725	725
Num. tumour type:		26	26	26	26	26	26

^∗p<0.05; ^∗∗p<0.01; ^∗∗∗p<0.001