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Table 1 Comparing L_RNA_scaffolder results with Zv_9 assembly

From: L_RNA_scaffolder: scaffolding genomes with transcripts

Type   Number
(i) Consistent Both order and orientation were consistent 5,980
(ii) Inversions More evidence for L_RNA_scaffoldera 20
More evidence for Zv_9b 0
  20
(iii) Relocations Correctable relocations 885
Errant relocations More evidence for L_RNA_scaffolder 98
More evidence for Zv_9 21
Uncertainc 102
  1,106
(iv) Translocations More evidence for L_RNA_scaffolder 43
More evidence for Zv_9 16
Uncertain 33
Contigs from two reference scaffolds 31
Contigs from one scaffold and one chromosome, respectively 137
  260
Total   7,366
  1. a Three approaches including syntenic block orders, human homolog coverage and zebrafish ‘guide’ transcript completeness, are used to determine the correct connection. The connection with the most evidence is regarded to be correct. For these cases, L_RNA_scaffolder results have more supporting evidence than Zv_9.
  2. b For these cases, Zv_9 connections have more supporting evidence than L_RNA_scaffolder results.
  3. c There is the same amount of evidence or no supporting evidence for both conflicting connections. It is hard to determine which connection is correct.