0: Reference 1: Alternate allele 2: Second alternate allele 3: Third alternate allele
ACAC/ACACAC. You only have two alternate alleles shown, so there should be no
3/? in there. This is basically a modified VCF format.
Note that in a valid VCF the ALT1 column would not exist, so your example would not be correct.
According to the VCF format specification, all the Alternate alleles are defined in the "ALT" column, separated by commas.
For example, your example would be:
CHROM POS REF ALT 1 2078 A ACACAC,ACAC
In this case, a genotype of 1 would mean ACACAC, and a genotype of 2 would represent ACAC.
In general, SNPs should always be bi-allelic variations, e.g. only two alleles are commonly found. In the close past, tri-allelic SNPs were generally filtered out, in order to simplify he downstream analysis. However, recently I've seen some tri-allelic SNPs being used in public datasets, so this may create some confusion in the future.