Method for encoding of quality values of a data structure, whereby said data structure comprises a set of genomic reads, whereby each genomic read includes - an actual sequenced nucleotide sequence as a local part of a donor sequence or genome, whereby said nucleotide sequence includes a sequence of symbols derived from a nucleotide alphabet, - a mapping position indicating an alignment of said nucleotide sequence relating to at least one reference nucleotide sequence of the donor sequence or genome, - a CIGAR string indicating similarities and/or differences of said nucleotide sequence relating to at least one of said reference nucleotide sequence, and - a sequence of quality values, each quality value is derived from a quality value alphabet, whereby a quality value at an index locus of said sequence of quality values is assigned to a corresponding symbol of said nucleotide sequence at said index locus and indicates a likelihood that the corresponding symbol is correct in view of at least one of said reference nucleotide sequences, wherein the method comprises the following steps executable by a data processing system: - providing a plurality of codebooks, each codebook is identified by a codebook identifier, whereby each codebook provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, - ascertain the quality values of each read covering a certain index locus, - determine a codebook identifier identifying a specific codebook from said plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each codebook provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, - quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and - encode all determined codebook identifiers using a first entropy encoder and encode all quantized quality values using a second entropy encoder or a set of encoders. - an actual sequenced nucleotide sequence as a local part of a donor sequence or genome, whereby said nucleotide sequence includes a sequence of symbols derived from a nucleotide alphabet, - a mapping position indicating an alignment of said nucleotide sequence relating to at least one reference nucleotide sequence of the donor sequence or genome, - a CIGAR string indicating similarities and/or differences of said nucleotide sequence relating to at least one of said reference nucleotide sequence, and - a sequence of quality values, each quality value is derived from a quality value alphabet, whereby a quality value at an index locus of said sequence of quality values is assigned to a corresponding symbol of said nucleotide sequence at said index locus and indicates a likelihood that the corresponding symbol is correct in view of at least one of said reference nucleotide sequences, - providing a plurality of codebooks, each codebook is identified by a codebook identifier, whereby each codebook provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, - ascertain the quality values of each read covering a certain index locus, - determine a codebook identifier identifying a specific codebook from said plurality of codebooks for said certain index locus based on the ascertained quality values of said certain index locus, whereby each codebook provides a mapping from a quality value of said quality value alphabet to a corresponding quantized quality value of a quantized quality value alphabet, - quantizing all ascertained quality values at said certain index locus using the specific codebook identified by the codebook identifier at said certain index locus in order to obtain for each quality value at said certain index locus a corresponding quantized quality value, and - encode all determined codebook identifiers using a first entropy encoder and encode all quantized quality values using a second entropy encoder or a set of encoders.