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Table 1 De novo assembly statistics for P. syringae

From: SOPRA: Scaffolding algorithm for paired reads via statistical optimization

Assembler

ε no _m

ε mis _m

N50

Genome coverage

 

% of total assembly

No. of events/Mbp of assembly

Kbp

%

S-SOPRA (unpaired)

.2

.14

.33

5.25

-

-

2.1

98.4

V-SOPRA (unpaired)

.17

.01

0

0

-

-

6.6

97.7

Velvet (unpaired)

.16

.01

0

0

-

-

7

97.2

S-SOPRA (paired)

.3

.13

.49

5.58

0.66

3.12

44.2

98.4

V-SOPRA (paired)

.18

.01

.33

0

0

0

74

97.7

Velvet (paired1)

.16

.02

3.28

.82

0

0.16

46.7

97.7

Velvet (paired2)

.14

.81

4.93

4.1

1.64

7.56

118.8

96.6

  1. The error rate εno _mrepresents the sum of length of the contigs/scaffolds with no BLAST hit as a percentage of total assembled bases. Mismatch error rate εmis _mreports the total number of mismatches and indels as a percentage of total assembled bases. The error rates and are associated with chimeric mis-assemblies, involving gaps smaller or larger than 500 bases, respectively. The error rate accounts for the number of cases where the relative orientation of two neighboring contigs disagrees with that in the reference genome. The cases where the estimated separation between two consecutive contigs on a scaffold differs from the real separation in the reference genome by more than 500 bases are associated with . These last four categories of errors are measure as the number of erroneous events per megabases of assembly.