Disclosed here is a method for the detection of a naturally occurring mutation in a target sequence in one or more members of a population, comprising: providing a plurality of pools of amplification products each comprising the target sequence amplified from genomic DNA of a subset of the one or more members of the population, wherein each pool of the amplification products shares a unique pool identifier; determining the nucleotide sequence of the amplification products using high throughput sequencing; and identifying mutations by clustering/aligning the sequences of the amplified products without the use of an enzyme which recognizes and cuts single nucleotide sequence mismatches and without performing heteroduplex analysis, and identifying the one or more members carrying the mutation using the pool identifier.