Table 2. Logistic regression of P-element copy number and structural variation with hybrid dysgenesis.

P-Element Estimate	P-Value (Full Data Set)	Association (Full Data Set)	P-Value (No DGRP-42)	Association (No DGRP-42)
Normalized coverage	3.55E−01	−	2.28E−05	+
TIDAL-total	2.03E−01	+	4.81E−02	+
TIDAL-weighted	2.81E−01	+	6.59E−05	+
TEMP-total	5.51E−01	+	6.36E−01	+
TEMP-weighted	7.99E−01	−	2.88E−01	−
HISAT/Cufflinks CN	9.36E−01	−	1.22E−05	+
HISAT/StringTie CN	3.49E−01	+	7.13E−04	+
gsnap/Cufflinks CN	5.81E−01	−	4.48E−05	+
gsnap/StringTie CN	3.54E−02	−	1.86E−02	+
STAR/Cufflinks CN	4.72E−06	−	2.67E−03	−
STAR/StringTie CN	4.53E−04	−	7.29E−01	+
HISAT/Cufflinks FL-CN	2.78E−05	−	6.94E−01	−
HISAT/StringTie FL-CN	9.20E−09	−	8.18E−05	−
gsnap/Cufflinks FL-CN	7.33E−02	−	1.75E−01	+
gsnap/StringTie FL-CN	8.60E−01	−	6.44E−01	+
STAR/Cufflinks FL-CN	4.49E−04	−	6.03E−01	−
STAR/StringTie CN	2.32E−04	−	8.44E−01	+
HISAT/Cufflinks FP/KP	2.88E−02	−	2.35E−01	−
HISAT/StringTie FP/KP	1.88E−02	−	6.16E−01	−
gsnap/Cufflinks FP/KP	6.79E−02	−	4.23E−01	−
gsnap/StringTie FP/KP	9.28E−01	+	6.51E−01	−
STAR/Cufflinks FP/KP	4.42E−01	+	3.21E−01	+
STAR/StringTie FP/KP	6.19E−01	−	8.51E−01	−

The fit of alternative models, which includes the indicated estimate of P-element abundance or structural variation as a fixed effect, were compared to nested null models. The P-values reported result from a likelihood ratio test comparing the two model fits, with a value of <0.05 indicating that the model including an estimate of P-element abundance or structural variation provided a significantly better fit to the data than the null model. For each model, the direction of the association between paternal P-elements and hybrid dysgenesis is also indicated (±). All model pairs were fitted to both the full data set and the data set excluding the outlier strain DGRP-42. Complete information about model components, fit, and comparison can be found in Table S6. CN, copy number; FL, full-length; FP, full-length P-element.