Mega2 v4.7.0 assumes trait is dichotomous by default when reading from a PLINK fam file.

[Dan Weeks]

When version 4.7.0 of Mega2 reads a set of binary PLINK files as input, it assumes that the trait locus in the fam file is an affection status locus by default.  If the trait locus in the fam file is a quantitative trait, Mega2 will misinterpret it, generating error messages like this:

Reading PLINK format ped file: bed.fam (6 columns)
ERROR: Line 1, column 5: Illegal affection status 21.2, setting to unknown.

Unfortunately, these error messages will quickly scroll off the screen, leaving the user unaware of these error messages.

Solution: If the trait locus is a quantitative trait, you should use the PLINK argument '--quantitative' within Mega2. 

[Dan Weeks]

When version 4.7.0 of Mega2 reads a PLINK file in 'ped' format, it assumes that the trait locus in the ped file is an affection status locus by default.  If the trait locus in the ped file is a quantitative trait, Mega2 will misinterpret it.