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Table 4 Comparative performance of PGA and GeSeq in annotating plastomes

From: PGA: a software package for rapid, accurate, and flexible batch annotation of plastomes

  Gymnosperms Angiosperms
GenBank GeSeq PGA GenBank GeSeq PGA
tRNAs lacking introns MG 2.20 0.75 0.10 0.10 0.15 0.00
WG 0.15 0.10 0.00 0.50 0.00 0.00
WGB 2.85 2.2 0.00 4.65 1.70 0.00
CG 21.60 23.70 26.60 24.00 27.40 29.25
tRNAs with introns ME 1.65 2.60 0.00 0.30 1.75 0.20
WE 0.10 0.00 0.00 0.50 0.00 0.00
WEB 2.20 2.55 0.00 3.30 1.80 0.00
CE 8.35 7.15 12.30 12.00 12.50 15.85
PCGs lacking introns MG 1.15 0.65 0.05 0.15 0.00 0.10
WG 0.10 0.05 0.05 0.00 0.05 0.10
WGB 0.40 35.65 0.55 0.45 23.00 0.10
CG 69.95 35.25 70.90 69.75 47.35 70.15
PCGs with introns ME 1.55 4.35 0.00 0.70 4.05 0.50
WE 0.00 0.00 0.00 0.05 0.00 0.10
WEB 7.90 14.70 0.15 11.60 16.55 0.05
CE 14.35 4.75 23.65 20.40 12.05 32.15
rRNAs MG 0.60 0.00 0.00 0.00 0.00 0.00
WG 0.00 0.00 0.00 0.00 0.00 0.00
WGB 2.25 2.55 0.05 2.60 0.90 0.00
CG 1.90 2.20 4.70 5.40 7.10 8.00
  1. Numbers represent mean values
  2. MG = missing annotated gene, WG = wrongly annotated gene, WGB = wrongly annotated gene boundary, CG = correctly annotated gene. ME = missing annotated exon, WE = wrongly annotated exon, WEB = wrongly annotated exon boundary, CE = correctly annotated exon