Big Y and a dreaded "No Call"

We've gotten the results from our second big Y Elmer testing pillar and...we have a problem. For a look at what we've been attempting to do see Adventures in Big Y and YSEQ and my partial return from YSEQ.

What could possibly be the problem? Okay, based on our YSTR testing, this is the breakdown we expect:

In that picture R1 and L2 are our known good trees. We want to find out where they match (which is important to identifying SNPs for Edward Elmer) but also where they mismatch (which is important to placing all the other men except G1 there).

So we're triangulating the Y SNPs.

L2 and M1 were tested first. M1 is an unknown. We're not sure whose line he's on, but we suspect Samuel Elmer because of his close STR match to R1.

This is basically where things stand with testers today:

At first, we only had M1 and L2. M1 had A2281 and L2 did not. Then R1 came along and he had A2281. Bonus. Things are lining up the way we thought, M1 and R1 have one SNP in common that L2 does not. So M1 and R1 are more closely related.

Enter confusion. M1 also has A2284 in common with L2. R1 does not have that. How can M1 carry one SNP from each branch of the family that the other branch does not have?

Then I noticed that L2's slot for A2281 was designated a "no call" which just means, nothing was returned. Not a negative, not a positive..just nothing.

Okay, so is A2284 a no call for R1 or is it a negative?

What is swinging in the balance is a big part of the reason we ran Big Y tests. We want to know which side M1 is on. 

If L2's no call turns out to be a positive for A2281, then it's another SNP shared by all the Elmers. If R1's missing entry for A2284 is a real negative, then that SNP is not shared by all Elmers and belongs to L2's family. That would rewrite the tree above for M1. He would be with me and L2. 

If L2's A2281 is a real negative and A2284 ends up positive for R1 then A2281 will be the SNP to watch and belongs on R1's line. That would rewrite the tree above and put me on R1's line instead of L2's. 

If both are positive, then we have a nice list of Ed Elmer's SNPs, but not much sorting closer to home can take place for M1...and possibly for me. 

Update 9/20/2015

The "no call" on A2281 for kit 369990 (aka L2) has been resolved. He is positive for A2281 like all the other Elmers. The question remains whether the Knowlton no call for that same SNP is really a positive or negative.