HCV NS3 Transactivated Protein 2 (NS3TP2)

TRA16 and GRAMD3, can be viewed by using the sample data set available at the TraceHaplotyper homepage. The TRA16 is an example of an indel followed by a single SNP. TraceHaplotyper is also able to analyze a situation in which two SNPs follow the indel. Haplotypes were constructed successfully for the GRAMD3 locus even when the SNP site was as much as 171 bp downstream from the site of the indel. However, the quality of the trace and base calling may affect the result because the program is not designed to contend with deviation from the expected pattern of more than one base. The program is unlikely to be able to align the expected and the trace sequences of low-quality traces with such deviations.