 sequencing reads are first transformed into a fastq file (more information about fastq files can be found <a href="http://hutchdatascience.org/Choosing_Genomics_Tools/sequencing-data.html">here</a> in the sequencing data chapter in the Quality Controls section. Then the sequencing reads are aligned to a reference genome to create a BAM file. This data is sorted and merged, and PCR duplicates are identified. The confidence that each read was sequenced correctly is reflected in the base quality score. This s