Hi -

If the VCF file was created with a reference genome, it may appear that some predicted variants are not mapped on the genome. If it was created without a reference genome, none of them are mapped.

When a variant is not mapped to a reference genome, the chrom field indicates the id of the prediction (here "INDEL_lower_path_2890") and the mapping position indicates the position of the variant (here an INDEL) on the sequence of the bubble of the variant. Actually, in this case, the CHROM field does not add any piece of information wrt the fasta file.

Hope this helps, Pierre