I have all those tools reporting the same coverage with JaCoCo: 69% line coverage and 23% branch coverage.
Note: Screenshots had been taken over several days so they have slightly different values, but the variance is < 1%
Jenkins: 
Maven: 
Eclipse: 
However Sonar reports different values:
Maven project is structured as follows:
- main (aggregator)
- java module
- js (node) module
You can see the same coverage reported on main and java modules, and no coverage for the js one.
I'm using the latest versions of jacoco, jacoco-maven-plugin and Sonar's Java Plugin.
Here are the relevant build log fragments from mvn sonar:sonar -- all seem to be in order:
$ egrep -i 'jacoco|\[warn]' consoleText [WARN] [04:34:29.569] 'sonar.dynamicAnalysis' is deprecated since version 4.3 and should no longer be used. [WARN] [04:34:29.576] 'sonar.dynamicAnalysis' is deprecated since version 4.3 and should no longer be used. [WARN] [04:34:29.593] 'sonar.dynamicAnalysis' is deprecated since version 4.3 and should no longer be used. [INFO] [04:34:32.704] JaCoCoItSensor: JaCoCo IT report not found: /home/acme/workspace/example-Sonar-DSL/modules/example-main/target/jacoco-it.exec [WARN] [04:34:32.952] Bytecode of dependencies was not provided for analysis of test files, you might end up with less precise results. Bytecode can be provided using sonar.java.test.libraries property [WARN] [04:34:50.101] Cobertura report not found at /home/acme/workspace/example-Sonar-DSL/modules/example-main/target/site/cobertura/coverage.xml [INFO] [04:35:03.391] Sensor JaCoCoSensor [INFO] [04:35:03.406] Analysing /home/acme/workspace/example-Sonar-DSL/modules/example-main/target/jacoco.exec [INFO] [04:35:03.712] Sensor JaCoCoSensor (done) | time=321ms [INFO] [04:35:03.712] Sensor JaCoCoOverallSensor [INFO] [04:35:03.714] Analysing /home/acme/workspace/example-Sonar-DSL/modules/example-main/target/jacoco.exec [INFO] [04:35:03.762] Analysing /home/acme/workspace/example-Sonar-DSL/modules/example-main/target/sonar/jacoco-overall.exec [INFO] [04:35:03.906] Sensor JaCoCoOverallSensor (done) | time=194ms [INFO] [04:35:11.013] JaCoCoSensor: JaCoCo report not found : /home/acme/workspace/example-Sonar-DSL/modules/frontend/target/jacoco.exec [INFO] [04:35:11.013] JaCoCoItSensor: JaCoCo IT report not found: /home/acme/workspace/example-Sonar-DSL/modules/frontend/target/jacoco-it.exec [INFO] [04:35:11.179] JaCoCoSensor: JaCoCo report not found : /home/acme/workspace/example-Sonar-DSL/target/jacoco.exec [INFO] [04:35:11.179] JaCoCoItSensor: JaCoCo IT report not found: /home/acme/workspace/example-Sonar-DSL/target/jacoco-it.exec Is this a bug in Sonar's Java Plugin? I think it's highly unlikely that metric reported by sonar is correct when 3 other tools configured by different people consistently show different values.
