GATK 4.1.4.0 Mutect stats output
This was answered by the OP -- it was a bug that has been fixed in a subsequent release, 4.1.5.0. See the release notes here: https://github.com/broadinstitute/gatk/releases/tag/4.1.5.0


  Made callable sites a Long to avoid integer overflow (#6303)


Issue ticket: https://github.com/broadinstitute/gatk/issues/6302