Table 2 Mixed effects models predicting the levels of six different measures of instability using the log number of SBS2 and SBS13 mutations and TP53 mutation status, as well as 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 10-15, 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

Count model: (Intercept)

Coefficient

5.37

4.44

0.257

3.16

0.581

1.62

95% CI

(−7.32,18.1)

(4.03,4.84)

(−1.36,1.87)

(2.67,3.65)

(−1.44;2.61)

(0.355,2.88)

p value

0.408

1.16×10^{−100∗∗∗}

0.755

3.04×10^{−41∗∗∗}

0.574

0.0121^∗

Count model: Age

Coefficient

0.0490

−0.000657

0.0281

0.00315

0.0235

−0.00354

95% CI

(−0.084,0.182)

(−0.00398,0.00267)

(0.00250,0.0537)

(−0.00049,0.00679)

(−0.00840,0.0554)

(−0.0130,0.00596)

p value

0.472

0.699

0.0314^∗

0.0903

0.149

0.465

Count model:

Coefficient

5.83

0.241

0.704

0.449

0.575

0.577

log(SBS2/13)

95% CI

(4.34,7.32)

(0.200,0.282)

(0.468,0.940)

(0.391,0.507)

(0.268,0.882)

(0.419,0.735)

p value

7.55×10^{−14∗∗∗}

1.20×10^{−30∗∗∗}

5.00×10^{−9∗∗∗}

3.03×10^{−45∗∗∗}

2.44×10^{−4∗∗∗}

8.07×10^{−13∗∗∗}

Count model: TP53

Coefficient

11.0

0.131

1.26

1.08

0.123

2.16

95% CI

(7.15,14.9)

(0.039,0.224)

(0.502,2.02)

(0.502,1.65)

(−0.024,0.271)

(0.258,4.07)

p value

3.70×10^{−8∗∗∗}

5.27×10^−3∗∗

0.00114^∗∗

2.37×10^{−4∗∗∗}

0.102

0.0260^∗

Count model:

Coefficient

−0.156

−0.158

−0.347

log(SBS2/13):TP53

95% CI

(−0.268,−0.045)

(−0.241,−0.0742)

(−0.622,−0.0729)

p value

0.00610^∗∗

2.17×10^{−4∗∗∗}

0.0131^∗

Count model:

Coefficient

-0.00462

−0.00354

Age:log(SBS2/13)

95% CI

(-0.00845,-0.000799)

(−0.00834,0.00126)

p value

0.0178^∗

0.148

Zero model: (Intercept)

Coefficient

−0.684

1.07

95% CI

(−0.839,−0.530)

(0.902,1.24)

p value

4.19×10^{−18∗∗∗}

4.23×10^{−36∗∗∗}

AIC

6710.3

10,058.3

8687.9

10448.8

6356.6

3266.8

Log likelihood

−3349.1

−5023.2

−4335.9

−5217.4

−3170.3

−1625.4

Num. obs.

725

725

717

725

725

725

Num. tumour types

26

26

26

26

26

26