A red background is used for men whose data has not yet been fully analyzed. His position on the tree is not yet final, and will in general be downstream of the current position. He may not be positive for all the SNPs/INDELs in the block he descends from.
Men whose NGS data have been fully analyzed are indicated with a grey background color.
Those men with a grey background and a pink bar to their left have been finalized, but haven't gone through as much scrutinity as earlier kits have. In particular, no search has been made for recurrent SNPs or other unusual mutations. For the vast majority of kits, this has no effect at all, but I will review them as necessary in the future.
A green SNP name with a '?' indicates that the SNP's status for the block is uncertain, but assumed to be positive. The same SNP probably occurs in an upstream block. It will be necessary to check BAM files or perhaps Sanger sequence some men to prove the result.
Mutations written with a red background fall within a region of the Y chromosome, such as the palindromic region, which has left the position of the mutation ambiguous. The true mutation may be at the indicated position, or at any one of a number of alternate positions.