The Nave's south aisle wall contains a common medieval stained glass theme: The Jesse tree, first seen in windows at the Saint-Denis Basilica north of Paris where the French Gothic movement started. While York's window (created 1310-1320) shares much of the iconic visuals of other Jesse Tree depictions, it has several unique characteristics: For one thing, the depiction of the vine is quite naturalistic and the vine encircles the "edge" figures in the side panels (Moses and the prophets). Also, Mary's position, size, and color are quite emphatic. Note the blue figure second from the top in the center panel below. Jesse, himself, lies at the bottom swathed in red.
The large windows of the Nave typically have three columns of seven sections as does this Jesse Window. Most of the other windows have strong horizontal bands to separate the sections but as the Jesse Tree is supposedly one vine (genealogical branch), the separation between panels is not well defined. The vine crawls from panel to panel, spanning the columns, and integrates Old Testament figures with the new.
The top three quatrefoil windows shown below were "restored" in 1789 with the inclusion of glass consistent with 18th century style and have nothing to do with the theme of the window. That was not the worst artistic sin as the restorers took too much license and rearranged the panels! Not a good thing to do when showing lineage which is the main point of a Jesse tree: to show that Jesus is a descendent of David, Jesse's father, through both Joseph and Mary. The 1950 restoration (note the date in the lower right hand corner in the picture above, had to recreate the lowest central panel where Jesse reclines in his redness and the branch stems from him.)
The Jesse Tree was defined in a prophecy of Isaiah (11:1-3 -- if you're keeping score): "And there shall come forth a shoot from the stump of Jesse, and a branch shall grow out of his roots....' Prophets usually climb up the side panels of a Jesse tree as we see here (in fact, here, they are entwined in the vine itself, and there are twelve of them, supposedly presaging the Apostles, another echo of the Old Testament in the New.) As shown in the central panels below, Jesus (excuse the albino head here) is on top of the tree, over his mother Mary, and her ancestors as described in the first chapter of the gospel of Matthew. The prophets on the side panels slightly lower than Jesus are Moses (not really a prophet) and Elijah.
The largest panel is the crowned Mary, Queen of Heaven. She's by herself here (often in Jesse Trees, she has the infant Jesus on her lap.) What's missing from the Jesse tree but found almost everywhere else is the dove representing the Holy Spirit. It's thought that a restoration wiped it out (it could be in the cross above Jesus' head or in the top quatrefoil window.