Increasing confidence of allele calls with molecular counting

A method for assessing the presence of an allele of a polymorphic target sequence in a tagged genomic sample, comprising:

• a) amplifying a population of different initial target DNA molecules from a tagged genomic sample thereby producing a population of amplified target DNA molecules, wherein the different initial target DNA molecules that comprise a polymorphic target sequence are tagged with different degenerate base region (DBR) sequences, wherein said DBR sequences comprises at least one nucleotide base selected from:
• R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof and wherein the amplified target DNA molecules comprise said polymorphic target sequence and an associated DBR sequence of said DBR sequences;
• b) sequencing a 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:
• (i) the nucleotide sequence of at least a portion of the polymorphic target sequence and (ii) the nucleotide sequence of an associated DBR sequence;
• c) assessing, using a computer, the presence of said allele in said tagged genomic sample, based on:
• (i) a determination of the number of said different DBR sequences that are associated with said allele;
• and
• (ii) a determination of the number of said sequence reads that comprise each of the different DBR sequences that are associated with said allele.