According to a study published yesterday, Revisiting the harem conspiracy and death of Ramesses III: anthropological, forensic, radiological, and genetic study, Y- STR data places his YDNA haplogroup in E1b1a using Whit Athey's Haplogroup predictor:
"Genetic kinship analyses revealed identical haplotypes in both mummies (table 1⇓); using the Whit Athey’s haplogroup predictor, we determined the Y chromosomal haplogroup E1b1a. "
his DYS repeats are listed as follows:
Plugging these numbers in Whit Athey's predictor does indeed indicate that his haplogroup is E1b1a with 99.1% probability using equal priors. The decisive DYS, to judge between E1b1a and E1b1b, is DYS 390, with the exclusion of DYS 390, his haplotype belongs to 83.7 % E1b1b and 15.8% E1b1a, however, it is well known that DYS 390 = 21 is a high probability signature for West/Central/Southern Africa, i.e. where E1b1a dominates (see below).
UPDATE : Upon receiving an e-mail stating that the haplotype could still belong to E1b1b, on the basis of a haplotype from Chad present in the FTDNA database that has DYS 390 = 21, I further looked into it, the presence of such a haplotype would not necessarily refute what the authors of this study are claiming, because if one enters the repeats for those Chad E1b1b haplotypes (but only for the same DYS#'s that are included this study) into the predictor, i.e. :
one would still get an assignment to haplogroup E1b1b with 88.6% probability and only a 5.6% probability that the haplotype may belong to E1b1a, therefore, I highly doubt that this pharaoh's haplotype, if extracted correctly and with out contamination, would be anything but E1b1a, absent an SNP test however, one can never be 100% sure.