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An isopycnal stream-coordinate analysis of velocity, transport, and potential vorticity (PV), recently applied to observations of the subsurface countercurrents (SCCs) in the equatorial Pacific Ocean, is applied here to the SCCs in a numerical general ocean circulation model, run by the Japan Marine Science and Technology Center (JAMSTEC). Each observed SCC core separates regions of nearly uniform potential vorticity: low on the equatorward side, high on the poleward side. Similar low-PV pools are found in the model, but the high-PV region poleward of the southern SCC is missing. The potential vorticity gradient in each core is weaker in the model than in observations, and relative vorticity plays only a minor role in the model. Its unusually high vertical resolution, with 55 levels, together with its weak lateral dissipation may be key factors in the JAMSTEC model's ability to simulate SCCs.