Fig. 1

The percentage of false SNV calls for using a different reference sequence. Full-length HBV genome sequence, Clone_N6 (KJ790199; genotype C, Taiwan) was cloned from a CHB patient and sequenced using a direct Sanger sequencer. This nucleotide sequence would be used as a standard sequence. Clone_N6 was also fragmented to be sequenced by NGS analysis. The mapping results of NGS reads from the Clone_N6 using the following mapping references: sample-specific reference, genotype specific reference (JN315779; genotype C, Asia) and incompatible genotype reference (FJ787477; genotype B, Asia). When compared with the standard sequence of Clone_N6, derived from direct sequencing, the percentage of false SNVs calls increased significantly from 0.09% using sample-specific reference as mapping reference to 28.95% using incompatible genotype reference as the mapping reference. ^aSample-specific reference is the consensus sequence obtained from the NGS reads of each sample through alignment with its same genotype mapping reference. ^bReference is using the same genotype as the sample (genotype C). ^cReference is using the incompatible genotype as the sample (genotype B)