Table 3

GAGE statistics (SNPs, indels and misjoins) on Staphylococcus aureus.

Assembler

SNPs

Indels < 5 bp

Indels ≥ 5 bp

Misjoins

Inv

Reloc


Allpaths-LG

79

4

12

4

0

4

MSR-CA

191

23

10

13

6

7


Allpaths-LG + MSR-CA

GAM-NGS

137

9

15

5

0

5

GAA

145

8

16

6

0

6

ZORRO

133

12

8

6

2

4


MSR-CA + Allpaths-LG

GAM-NGS

214

19

10

9

2

7

GAA

206

22

15

11

2

9

ZORRO

262

24

9

7

4

3



Allpaths-LG

79

4

12

4

0

4

SOAPdenovo

247

25

31

15

1

14


Allpaths-LG + SOAPdenovo

GAM-NGS

88

5

14

4

0

4

GAA

100

9

19

10

1

9

ZORRO

227

19

12

6

1

5


SOAPdenovo+ Allpaths-LG

GAM-NGS

304

27

29

15

1

14

GAA

314

32

30

12

1

11

ZORRO

299

28

11

13

2

11


For each assembly we show the number of SNPs, the number of indels shorter than 5 bp and greater (or equal) than 5 bp. The number of misjoins is computed as the sum of inversions (parts of contigs reversed with respect to the reference genome) and relocations (rearrangements moving a contig within/between chromosomes).

Vicedomini et al. BMC Bioinformatics 2013 14(Suppl 7):S6   doi:10.1186/1471-2105-14-S7-S6

Open Data