Short-term genome evolution of Listeria monocytogenes in a non-controlled environment

BMC Genomics

Table 2 Assembly quality metrics for strains sequenced in this study

Strain	F6900	J0161	J2818	FSL J1-194
Contig N50⁽¹⁾	434 kb	148 kb	167 kb	156 kb
Total contigs	35	49	38	43
Assembly size	2.96 Mb	2.97 Mb	2.97 Mb	2.93 Mb
Aligned sequence length (nt)⁽²⁾	2,921,655	2,921,243	2,921,377	-
comK prophage sequence length (number of contigs)⁽³⁾	38,876 bp (5)	41,349 bp (4)	42,001 bp (2)	42,189 bp (1)
Contigs to capture 90% of assembly	11	19	19	19
Fraction bases Q40⁽⁴⁾	99.5%	99.7%	99.8%	99.7%
Fraction reference covered	95.97%	95.97%	96.08%	93.79%
Assembled coverage	25×	30×	24×	22×

⁽¹⁾ Length-weighted median that describes the contig size in which at least half the bases reside.
⁽²⁾ Length of each sequence in the refined alignment containing the 1988 and 2000 isolates. The length for F6854 is 2,921,388 nt.
⁽³⁾ Sequenced length of the prophage inserted into comK for each isolate/strain. The length for F6854 is 41,259 nt.
⁽⁴⁾ As reported by 454 assembly software.

ISSN: 1471-2164