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Table 5 Number of single-nucleotide variants (SNVs) obtained by mapping of mRNA-seq data from A. thaliana against the TAIR10 reference genome sequence

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

 

Cov. Positions

SNVs

SNVs/Mbp

a

 Col-0 (CN)

9,098,019

24

3

 Col-0 (DE)

10,839,185

12

1

 Col-0 (JP)

12,819,475

18

1

 Col-0 (MX)

10,992,622

20

2

 Col-0 (NL)

11,479,175

23

2

 Col-0 (US)

12,320,980

21

2

b

 No-0 (DE)

13,205,980

22,006

1,666

 Sf-2 (ES)

13,174,328

23,169

1,759

 Can-0 (ES)

13,095,023

28,515

2,178

 Edi-0 (GB)

13,198,944

22,051

1,671

 Bur-0 (IE)

13,172,042

25,137

1,908

 Ct-1 (IT)

13,207,544

23,498

1,779

 Tsu-0 (JP)

13,205,663

21,836

1,654

 Mt-0 (LY)

13,220,021

21,953

1,661

 Kn-0 (LT)

13,185,117

23,141

1,755

 Hi-0 (NL)

13,212,525

19,123

1,447

 Ler-0 (PL)

13,216,378

21,857

1,654

 Ws-0 (RU)

13,194,655

22,999

1,743

  1. Only variants in coding exons were considered. Covered positions: positions with a minimum coverage of 4x; SNVs: total number of variants detected in coding regions; SNVs/Mbp: number of variants per Megabase of coding sequence. a) mRNA-seq data from A. thaliana ecotype Col-0 mapped against TAIR10. Provenance of each accession is indicated: China (CN), Taiwan (TW), Japan (JP), Mexico (MX), Netherlands (NL), United States of America (US). b) mRNA-seq data from Col-0 “NL” mapped on genome assemblies from thirteen different wild-derived A. thaliana accessions. Ecotype name and country of origin is indicated. Country codes: Germany (DE), Ireland (IE), Italy (IT), Japan (JP), Libya (LY), Lithuania (LT), Netherlands (NL), Norway (NO), Poland (PL), Russia (RU), Spain incl. Canary islands (ES), United Kingdom (GB)
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BMC Genomics

ISSN: 1471-2164

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