Method for preparing a counter-tagged population of nucleic acid molecules

A method of sequencing, comprising:

• a) amplifying a population of distinct initial target DNA molecules from a tagged genomic sample thereby producing a population of amplified target DNA molecules, wherein the distinct initial target DNA molecules that comprise a polymorphic target sequence are tagged with:
• (i) different degenerate base region (DBR) sequences, wherein said DBR sequences comprise at least one nucleotide base selected from:
• R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof and (ii) a unique multiplex identifier (MID) sequence that identifies a source for each of the initial target DNA molecules to which it is associated, and wherein each of a plurality of the amplified target DNA molecules comprises said polymorphic target sequence, an associated DBR sequence of said different DBR sequences and said unique MID sequence;
• and
• b) sequencing the plurality of the amplified target DNA molecules, thereby producing a plurality of sequence reads, wherein the sequencing step provides, for each of the amplified target DNA molecules that are sequenced:
• the nucleotide sequence of:
• (i) at least a portion of the polymorphic target sequence;
• (ii) an associated DBR sequence of said DBR sequences;
• and (iii) said unique MID sequence.