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Table 2 Single nucleotide variations statistics for the S. incanum and S. aethiopicum transcriptomes

From: Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

SNVs intraspecific variations INDELs SNPs Total SNVs
  S. incanum 535 11,861 12,396
   filtered 28 385  
  S. aethiopicum 4,556 159,571 164,127
   filtered 312 5,804  
  S. melongena 120 2,660 2,780
   filtered 6 57  
  S. torvum 6,318 18,829 25,147
   filtered 26 90  
SNVs interspecific variations INDELs SNPs Total SNVs
  S. incanum and S. aethiopicum 586 14,576 15,162
   filtered 29 649  
  S. incanum and S. melongena 3,673 102,104 105,777
   filtered 253 4,184  
  S. incanum and S. torvum 96,799 491,965 588,764
   filtered 760 3,995  
  S. aethiopicum and S. melongena 2,392 73,059 75,451
   filtered 165 3,277  
  S. aethiopicum and S. torvum 83,106 420,685 503,791
   filtered 604 3,229  
  S. melongena and S. torvum 92,323 464,071 556,394
   filtered 722 3,682  
  S. incanum, S. aethiopicum and S. melongena 108 41 149
   filtered 8 2  
  S. incanum, S. aethiopicum and S. torvum 908 198 1,106
   filtered 10 3  
  S. incanum, S. melongena and S. torvum 8,022 1,265 9,287
   filtered 118 15  
  S. aethiopicum, S. melongena and S. torvum 6,986 886 7,872
   filtered 102 12  
  S. incanum, S. aethiopicum, S. melongena and S. torvum 50 0 50
   filtered 2 0  
  1. SNVs (SNPs and INDELs) have been identified by the Freebayes SNP caller. The interspecific and intraspecific variations, as well as all species combination, have been determined by filtering ID (identification) species number. Every species and species comparison present an unambiguous identification number. The INDELs have been separated from SNPs applying the VKF filter to the total SNVs. The filtered SNPs and INDELs have been obtained by adding the CS60, HV0.05, CL60 and CEF filters
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BMC Genomics

ISSN: 1471-2164

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