The command ntpq -c 'rv 0 offset' can be used to retrieve
the current estimated time offset with nanosecond resolution, e.g.:
ntpq -c 'rv 0 offset' offset=-0.000032
Please note the offset value is displayed in milliseconds,
so in the example above the offset is 32 nanoseconds.
Extending the displayed offset from microsecond (up to at least ntp-4.2.6p5) to nanosecond resolution
(somewhere in ntp-4.2.8) has been discussed on the
NTP hackers mailing list:
and earlier.
— Martin Burnicki martin.burnicki@meinberg.de 2019-06-14