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Table 2 Simulated ancient DNA based on the REL606 E. coli genome

From: SNPest: a probabilistic graphical model for estimating genotypes

 

SNPest, standard model

SNPest, damage model

 

Bowtie2

BWA-PSSM

Bowtie2

BWA-PSSM

Depth

All

QC

All

QC

All

QC

All

QC

5

198

11

763

80

66

0

236

4

10

55

0

184

0

51

0

154

0

20

55

0

183

0

51

0

154

0

30

55

0

183

0

51

0

154

0

40

55

0

183

0

51

0

154

0

50

55

0

183

0

51

0

154

0

60

55

0

183

0

51

0

154

0

  1. Read lengths of 36 bp and an average depth of 27X was simulated, and DNA damage was simulated in the reads as described in the main text. SNPest was run in the haploid mode, without using the reference genome, and both with and without the damage model.