Table 2.
Assembly statistics, genomic features and predicted number of insertion sequence (IS) elements of the three S. sonnei isolates and one S. flexneri 3a isolate. Genomes were constructed with Flye, where Illumina short reads were utilised to polish a draft long-read assembly to yield a more complete and accurate final assembly
|
Isolate ID |
598 080 |
607 387 |
888 048 |
893 916 |
|---|---|---|---|---|
|
Species |
S. flexneri 3a |
|||
|
MLST |
152 |
152 |
245 |
152 |
|
Total contigs |
6 (2 Chromosomal contigs, 3 plasmids, 1 likely plasmid contig) |
37 (24 likely Chromosomal contigs, 4 plasmids, 9 likely plasmid contigs) |
5 (1 Chromosomal contig, 2 plasmids, 2 likely plasmid contigs) |
4 (1 Chromosomal contig, 3 plasmids) |
|
Total size (bp) |
5 282 682 |
5 315865 |
4 839 032 |
5 196 904 |
|
Largest contig (bp) |
4 879 016 |
2 500 534 |
4 519 004 |
4 813 904 |
|
N50 |
4 879 016 |
897 518 |
4 519 004 |
4 813 904 |
|
L50 |
1 |
2 |
1 |
1 |
|
GC content (%) |
50.86 |
50.82 |
50.68 |
50.84 |
|
Total CDS |
5533 |
5554 |
5174 |
5462 |
|
rRNA |
22 |
22 |
23 |
22 |
|
tRNA |
102 |
101 |
98 |
96 |
|
tmRNA |
1 |
1 |
1 |
1 |
|
Acquired resistance genes (ResFinder) |
11 |
9 |
7 |
11* |
|
Resistance genes (CARD)† |
59 |
58 |
47 |
60 |
|
Virulence factors (VFDB) |
14 |
13 |
12 |
13 |
|
Predicted IS number |
577 |
520 |
504 |
588 |
|
Estimated different IS |
45–48 |
38–43 |
43–47 |
43–44 |
|
SRR number (Illumina) |
SRR7842065 |
SRR7892120 |
SRR11096691 |
SRR11206407 |
|
SNP address |
1.3.197.460. 1360.1582. 2770 |
1.3.197.460. 1360.1582. 2813 |
35.43.43. 43.1189. 2224.2978 |
1.1.1.1.377. 394.3945 |
*Two mutations in gyrA are counted as two genes.
†Perfect and Strict hits only, total includes those also found by ResFinder.