/usr/share/circos/tools/matrix/matrix.missing.txt is in circos-tools 0.22-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | # 3 x 5 matrix, with missing values
r1 c1 11
r2 c1 21
r1 c2 12
r3 c2 32
r2 c3 23
r3 c3 33
r3 c4 34
r1 c5 15
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