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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)