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. Author manuscript; available in PMC: 2017 May 16.
Published in final edited form as: Virus Res. 2017 Feb 17;232:123–133. doi: 10.1016/j.virusres.2017.02.007

Table 2.

Evaluation of the effects of sequencing platform and RT-PCR on whole genome sequences

Sample designation Total length (nucleotides) Number and nature of non-conserved bases Position in sequence alignment Sequencing platform used: on PCR1 Sequencing platform used: on PCR2
Group 1
ME.2013.0131 11924 0 Both1 -
NB.2014.0941 11924 0 Both1 -
NY.2004.2473 11924 0 Both1 -
ON.2005.4941 11925 1, R by both reads 6880 Both2 -
VT.2006.0225 11923 1, R by Illumina, G by Sanger 4302 Both2 -
VT.2011.0122 11923 1, G by Illumina, K by Sanger 3780 Both1 -
Group 2
ON.2003.1519 11925 0 Illumina2 Sanger1
ON.2003.2760 11925 0 Illumina1 Sanger1
VT.2006.0259 11924 0 Sanger1 Sanger4
VT.2007.0522 11925 1, G (PCR1), R (PCR2) 4308 Illumina3 Sanger4
VT.2008.0209 11925 0 Sanger1 Sanger4
VT.2008.0237 11923 1, R (PCR1), G (PCR2) 4894 Sanger1 Sanger4
VT.2011.0122 11923 0 Illumina1 Sanger4
1

amplified as three fragments A, B, C

2

amplified as four fragments A1, A2, B, C

3

amplified as four fragments A, B C1 and C2

4

amplified as six fragments A1, A2, B1, B2, C1, C2