The percentage is equivalent to 100*used/total, as you imagined.

The percentage is 100*(1-available/total), confusingly different from 100*used/total.

Here, "available" means the same as shown in free.

Related threads:

• Meaning of "available" field in "free -m" command
• How shall I understand the output of free?

Reference manual

The behavior is documented in the reference manual.

In the alternate memory display modes, two abbreviated summary lines are shown consisting of these elements:

               a    b          c
    GiB Mem : 18.7/15.738   [ ... ]
    GiB Swap:  0.0/7.999    [ ... ]

Where: a) is the percentage used; b) is the total available; and c) > is one of two visual graphs of those representations.

In the case of physical memory, the percentage represents the total minus the estimated avail noted above. The `Mem' graph itself is divided between the non-cached portion of used and any remaining memory not otherwise accounted for by avail. See topic 4b. SUMMARY AREA Commands and the `m' command for additional information on that special 4-way toggle.

Source code of top

As of now, it can be verified by investigating the source code.

Data passed to the graph view

#ifdef MEMGRAPH_OLD
      my_misc = my_qued;
#else
      my_misc = MEM_VAL(mem_TOT) - MEM_VAL(mem_AVL) - my_used;
#endif
      Graph_mems->total = MEM_VAL(mem_TOT);
      Graph_mems->part1 = my_used;
      Graph_mems->part2 = my_misc;

Calculation in the graph view

   if (these->total > 0)
      scale = 100.0 / these->total;
   rx.pcnt_one = scale * these->part1;
   rx.pcnt_two = scale * these->part2;
   if (rx.pcnt_one + rx.pcnt_two > 100.0 || rx.pcnt_two < 0)
      rx.pcnt_two = 0;
   rx.pcnt_tot = rx.pcnt_one + rx.pcnt_two;

Data passed to the default view

      prT(bfT(0), mkM(MEM_VAL(mem_TOT))); prT(bfT(1), mkM(MEM_VAL(mem_FRE)));
      prT(bfT(2), mkM(MEM_VAL(mem_USE))); prT(bfT(3), mkM(my_qued));
      prT(bfT(4), mkM(MEM_VAL(swp_TOT))); prT(bfT(5), mkM(MEM_VAL(swp_FRE)));
      prT(bfT(6), mkM(MEM_VAL(swp_USE))); prT(bfT(7), mkM(MEM_VAL(mem_AVL)));

      snprintf(row, sizeof(row), N_unq(MEMORY_line1_fmt)
         , scT(label), N_txt(WORD_abv_mem_txt), bfT(0), bfT(1), bfT(2), bfT(3));
      Msg_row += sum_see(row, mem2UP);

On the reported inconsistency

• Did you check if your snapshots that you're matching are produced at the same system state? If printed at the same time, the used memory might be just 88.7% even in the default view.
• What is the version of your top? The current behavior of memory window has been introduced in 3.3.10.
• Which platform are you running it on? It seems there are some flags that can change the data passed to graph.

Corrected after further information and reveiw.