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Table 3 Simulated ancient DNA based on the REL606 E. coli genome

From: SNPest: a probabilistic graphical model for estimating genotypes

 

GeMS

FreeBayes

 

Bowtie2

BWA-PSSM

Bowtie2

BWA-PSSM

Depth

All

QC

All

QC

All

QC

All

QC

5

88

32

298

97

    

10

55

15

178

46

    

20

55

15

177

46

    

30

55

15

177

46

    

40

55

15

177

46

    

50

55

15

177

46

    

60

55

15

177

46

2808

0

2680

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. GeMS and FreeBayes were both run in haploid mode, GeMS with varying maximum read depths, and FreeBayes using all data.
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BMC Research Notes

ISSN: 1756-0500

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