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Table 3 Number of single-nucleotide variants (SNVs), number of insertion/deletion variants (indels) and transition/transversion (Ti/Tv) ratio for each comparison performed

From: Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

Line

SNVs

Indels

Ti/Tv

a

 ΔXT/FT vs Nb-1

117,278

7,626

1.4

 WT vs Nb-1

127,976

8,257

1.4

 Nb-1 vs Nb-1

56,930

4,505

1.3

b

 ΔXT/FT vs Nb-1

96,510

6,605

1.4

 WT vs Nb-1

106,079

7,217

1.4

 Shared

57,362

2,478

1.4

 ΔXT/FT unique

39,148

4,127

1.4

 ΔXT/FT unique (CDS)

3,036

80

1.8

  1. a) Raw number of variants before filtering out consensus errors, and b) after filtering out consensus errors, including subsets of variants relevant in the analysis. “Shared”: variants shared between ΔXT/FT and WT relative to Nb-1. “ΔXT/FT unique”: variants found only in ΔXT/FT relative to Nb-1. “ΔXT/FT unique (CDS)”: variants found only in ΔXT/FT relative to Nb-1 restricted to coding regions
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BMC Genomics

ISSN: 1471-2164

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