The difference is between "mark" and "deep". A sounding-line had a number of knots or artefacts attached to it a fathom apart which could be readily distinguished by feel, even when the leadsman's hands were cold. Because there are limits to the weight you can use in such a line, no more than 6 fathoms, or six "marks" had the distinguishing artefacts. So, "by the mark, five" or "by the mark, twain" called out by the leadsman told the skipper that the line had gone down that far. "By the deep, six" meant "deep or deeper than six fathoms", because beyond that, the depth really didn't matter, since even the first-rate sailing ships of the day drew no more than about 20 feet.. The soundings were carried out by a reliable, or "leading" hand. It was important to get it right, obviously, to prevent the ship from running aground. But in the navies of the world, losing a ship is a court-martial affair regardless of circumstance. Losing a ship through running aground was just about the worst thing a captain could do, so the ship - and the captain's fate - were very much in the hands of the leading hand.

HTH!