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@Ingolifs's answer to the question What was the last message to Opportunity today (13 Feb '19)? quotes ArsTechnica's Opportunity did not answer NASA’s final call, and it’s now lost to us:

Late Tuesday night, scientists at NASA's Jet Propulsion Laboratory sent their final data uplink to the Opportunity rover on Mars. Over this connection, via the Deep Space Network, the American jazz singer Billie Holiday crooned "I'll Be Seeing You," a song that closes with the lines...

To me, "Billie Holiday crooned..." suggests that a real audio recording of music was used to modulate the carrier in some way either direct AM or FM, or as digital data via more standard DSN data encoding schemes.

Is there any information available about how it was modulated or encoded?

uhoh
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TLDR; They didn't.

I submitted NASA FOIA request 19-JPL-F-00295 asking about this, and they responded:

[...] JPL confirmed that the song was not radiated to the spacecraft. It was just played on someone’s laptop in mission control as the transmission began.

So it seems the original story's information had sifted through one too many people or stretched the facts a little bit.

Relevant page of the response:

19-JPL-F-00295 Page 1

Mark Omo
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    wow. thoughts and prayers, shocked and saddened. Thank you very much for looking into this. I was hoping to lear about some special NASA DSNMP3 encoding scheme. – uhoh Mar 08 '19 at 16:23
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    I really did mean "hear about", not "lear about" ;-) – uhoh Mar 08 '19 at 23:21