On a hand Lead Line ( to explain, a length of rope with markings at various depths and a leaden weight on the end, used for taking Soundings) The marks differed so that the Leadsman could differentiate what they were even in the dark.
For instance, at 2 Fathoms a piece of cord with 2 knots tied in it.
3 fathoms three strips of leather
5 Fathoms a piece of white Flannel material..... and so on.
Not all depths were marked, so the Leadsman swinging the lead would call, " By the mark 5 " meaning 5 Fathoms were indicated on the lead line.
There was no mark at 6 fathoms, so he would call " Deep 6 " if the line came up wet somewhere between 5 and 7 fathoms.
So Deep six is somewhere in the sea without a mark, Deep 6 it, chuck it overboard somewhere.....