I've found a post explaining strand designations for some Illumina systems:

https://www.illumina.com/documents/products/technotes/technote_topbot.pdf

So the way they explain it is some local designation which is robust to reference genome build rearrangements. What confuses me is the supplementary of the following paper:

http://europepmc.org/articles/PMC3193030/bin/NIHMS322935-supplement-1.doc

In Table 1 they list this as exclusion criteria on Illumina 370CNV:

Call rate <97%, HWE p<1-6, MAF <1%, Mishap p<1-9, A/T and G/C SNPs, Mismatches between Illumina, dbSNP and/or HapMap position

Why would anyone exclude A/T and G/C SNPs? (Also, what is mishap?)

Thanks in advance!