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I was including odometry from wrong ekf node into navsat. The launch file with better results:

  <node pkg="robot_localization" type="ekf_localization_node" name="ekf_map" clear_params="true">
    <remap from="odometry/filtered" to="odometry/filtered_map"/>
  </node>

  ....

  <node pkg="robot_localization" type="navsat_transform_node" name="navsat_transform" clear_params="true>
    <remap from="odometry/filtered" to="odometry/filtered_map"/>
  </node>