Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections

BMC Genomics

Table 3 Error rates introduced by long range PCR and/or sequencing

Sequencing platform	Quality trimming	Input DNA	Substitutions*	Deletions*	Insertions*	Substitutions per nucleotide*
						A	C	G	T
PacBio	pError 0.01	amplicons	0.083	0.06	0.289	0.115	0.054	0.061	0.111
		non-enriched	0.015	0.051	0.204	0.015	0.013	0.017	0.014
PacBio	pError 0.001	amplicons	0.081	0.018	0.077	0.110	0.052	0.062	0.108
		non-enriched	0.009	0.012	0.029	0.009	0.006	0.010	0.008
Illumina	pError 0.01	amplicons	0.163	0.005	0.002	0.242	0.096	0.089	0.240
		non-enriched	0.083	0.004	0.001	0.091	0.077	0.078	0.090
Illumina	pError 0.001	amplicons	0.120	0.004	0.001	0.182	0.071	0.067	0.171
		non-enriched	0.027	0.004	0.001	0.028	0.025	0.027	0.028

*Error rate is the percentage of mismatches of the total number of bases mapped to the reference sequence. Error rates are means of two distinct input DNAs (Merlin and TB-BAC4-luc, and two amplicons (F1.1 + F3, respectively)

ISSN: 1471-2164