The data set Data1 has been received from HCV Research Group in Institute of Biomedical Research, at University of Birmingham. Data1 contains 30,927 reads obtained from the 5.2kb-long fragment of HCV-1a genome (which is more than a half of the entire HCV genome). The average (aligned) read length average is 292bp but it significantly varies as well as the depth of position coverage (see Additional File 1 for details). The depth of reads coverage variability is due to a strong bias in the sequence start points, reflecting the secondary structure of the template DNA or RNA used to generate the initial PCR products. As a result, shorter reads are produced by GC-rich sequences. Data1 is available upon request from the authors.