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Something doesn't add up then, the listed elevation for SFO is 13.1 ft MSL. http://www.airnav.com/airport/KSFO

UPDATE: tolerances around GL are 20 ft https://www.ecfr.gov/cgi-bin/retrieveECFR?gp=&SID=&r=PART&n=...

"...the minimum altitude recorded on the FDR was 59 feet above ground level." [emphasis added]

AGL (elevation above ground level), not MSL (elevation above mean sea level). The runway/taxiway elevation is already taken into account. They were 59 feet above the taxiway.

Also, they might not have been directly above the A340 at lowest altitude.

They were very close. See [1]. They were over the centerline of taxiway C, and 85 feet AGL crossing taxiway W. Minimum altitude was 2.5 secs later. There were three planes ahead, an A-340, a B-787 (also 55 feet high at the tail), and some UAL jet of about the same size.

A few feet lower and there would have been a collision.

[1] https://ntsb.gov/investigations/Pages/DCA17IA148.aspx

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