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. 2017 Mar 17;7(5):1487–1497. doi: 10.1534/g3.117.040634

Table 3. Logistic regression of P-element copy number and structural variation with hybrid dysgenesis after accounting for differences in hobo-abundance.

P-element Estimate hobo Estimate P-Value (Full Dataset) Association (Full Dataset) P-Value (No DGRP-42) Association (No DGRP-42)
Normalized coverage Normalized coverage 2.73E−01 8.59E−05 +
TIDAL-total Normalized coverage 5.03E−03 + 2.17E−07 +
TIDAL-weighted Normalized coverage 2.12E−01 + 4.75E−05 +
TEMP-total Normalized coverage 2.83E−01 + 4.97E−01 +
TEMP-weighted Normalized coverage 9.28E−01 3.66E−01
HISAT/Cufflinks CN Normalized coverage 5.63E−01 2.15E−04 +
HISAT/StringTie CN Normalized coverage 3.74E−01 9.43E−04 +
gsnap/Cufflinks CN Normalized coverage 3.32E−01 3.44E−04 +
gsnap/StringTie CN Normalized coverage 1.34E−02 5.96E−02 +
STAR/Cufflinks CN Normalized coverage 7.37E−05 1.19E−02
STAR/StringTie CN Normalized coverage 3.61E−04 8.72E−01 +
HISAT/Cufflinks FL-CN Normalized coverage 3.99E−05 6.77E−01
HISAT/StringTie FL-CN Normalized coverage 5.10E−07 8.41E−04
gsnap/Cufflinks FL-CN Normalized coverage 1.03E−01 1.47E−01 +
gsnap/StringTie FL-CN Normalized coverage 3.21E−01 1.68E−01 +
STAR/Cufflinks FL-CN Normalized coverage 1.32E−03 7.46E−01
STAR/StringTie FL-CN Normalized coverage 3.65E−04 8.54E−01 +
HISAT/Cufflinks FP/KP Normalized coverage 2.23E−01 7.24E−01
HISAT/StringTie FP/KP Normalized coverage 1.02E−02 4.57E−01
gsnap/Cufflinks FP/KP Normalized coverage 7.46E−02 4.47E−01
gsnap/StringTie FP/KP Normalized coverage 9.79E−02 6.16E−01
STAR/Cufflinks FP/KP Normalized coverage 1.06E−06 + 7.75E−08 +
STAR/StringTie FP/KP Normalized coverage 7.08E−01 2.54E−01 +

The fit of null models that include hobo abundance as a fixed effect and experimental block as a random effect was compared to alternative models that also include an estimate of P-element abundance or structural variation. 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 RAL-42. Complete information about model components, fit, and comparison can be found in Table S8. CN, copy number; FL, full-length; FP, full-length P-element.