Table 2. . Tandem repeat copy number variation in Mycoplasma pneumoniae genomes based on next-generation sequencing data.
|
Isolate† |
P1 type‡ |
Repeat copy number at VNTR loci§ |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mpn1 | Mpn13 | Mpn14 | Mpn15 | Mpn16 | P1-AGT | Mpn003 | Mpn103 | Mpn444 | Mpn651 | Mpn108a | Mpn108b | Mpn111 | ||
| 85138 |
1 |
6, 4, 5, 3 |
4 |
5 |
7 |
2 |
7, 6, 8 |
2 |
2 |
6, 5 |
1 |
9, 10, 8 |
7 |
10, 9 |
| 85084 |
1 |
7, 6, 4, 5, 8 |
4 |
5 |
7 |
2 |
7, 8, 6 |
2 |
2 |
5, 4, 6 |
1 |
9, 10, 8, 11 |
7 |
10 |
| M129-a |
1 |
4, 5 |
4 |
5 |
7 |
2 |
7, 8, 6 |
2 |
2 |
4, 5 |
1 |
8, 9, 7, 6 |
7 |
10 |
| 54524 |
1 |
4, 5 |
4 |
5 |
7 |
2 |
8, 7, 9 |
2 |
2 |
4, 3 |
1 |
9, 10, 8, 11 |
7 |
10 |
| 54089 |
1 |
3, 4 |
4 |
5 |
7 |
2 |
5 |
2 |
2 |
4 |
1 |
10, 9, 11, 8 |
7 |
10, 9 |
| 51494 |
1 |
4, 3, 5 |
4 |
5 |
7 |
2 |
8, 7, 9, 6, 5 |
2 |
2 |
4, 3, 5 |
1 |
6, 7, 5 |
7 |
10 |
| 1428 |
1 |
4, 3 |
4 |
5 |
7 |
2 |
7, 6, 8 |
2, 1 |
2 |
4 |
1 |
10, 11, 9 |
7 |
10 |
| S355 |
1 |
6, 4 |
4 |
5 |
7 |
2 |
9, 8, 10 |
2 |
2 |
5, 4 |
1 |
6 |
7 |
10 |
| C267 |
1 |
5, 6, 3 |
4 |
5 |
7 |
2 |
7, 8, 6 |
2, 1 |
2 |
5 |
1 |
7, 8, 6 |
7 |
10, 9 |
| 1145 |
1 |
5, 4 |
4, 3 |
5 |
7 |
2 |
12, 11, 13 |
2 |
2 |
4 |
1 |
8, 7, 10 |
7 |
10, 9 |
| 6250 |
1 |
4, 5, 6, 2 |
4 |
5 |
7 |
2 |
9, 8, 10 |
2 |
2 |
4, 5 |
1 |
8, 9, 7 |
7 |
10 |
| 4802 |
1 |
4 |
4 |
5 |
7 |
2 |
6, 7 |
2 |
2 |
4, 3 |
1, 2 |
9, 8, 7 |
7 |
10 |
| 5392 |
1a |
3 |
4 |
5 |
7 |
2 |
10 |
2 |
2 |
4, 3 |
1 |
9, 8, 10 |
7 |
10 |
| 2882 |
2 |
4 |
3 |
6 |
6 |
2 |
6, 5 |
1 |
3 |
3 |
2 |
7 |
14, 15 |
12 |
| 4358 |
2 |
2, 3 |
2 |
6 |
6 |
2 |
6 |
1 |
3 |
3 |
2 |
8, 9, 7 |
16, 15, 17 |
18, 17, 19, 16 |
| 309 |
2a |
7, 8, 5, 6, 4, 3 |
3 |
5 |
6 |
2 |
7, 6 |
1 |
3 |
3 |
2 |
7, 6 |
17, 15, 16, 18, 14 |
10 |
| M2592 |
2 |
3, 4 |
33 |
5 |
6 |
2 |
7, 8, 6, 9 |
1 |
3 |
3 |
2 |
7, 6, 8 |
20, 19, 21, 18 |
13, 12 |
| M2192 |
2 |
4, 5 |
3 |
6 |
6 |
2 |
7, 6 |
1 |
3 |
3 |
2 |
9, 10, 8 |
15, 14, 16, 13 |
17, 16, 18, 15 |
| M1139 |
2 |
5, 6 |
3 |
6 |
6 |
2 |
7, 8, 6 |
1 |
3 |
3 |
2 |
9, 10, 8 |
12, 11, 13 |
15, 14, 16 |
| PO1 |
2 |
4, 5 |
3, 4 |
6, 5, 7 |
6 |
2 |
6, 7, 5 |
1 |
3 |
3 |
2 |
7, 8 |
15, 14, 16 |
12 |
| MAC |
2 |
5, 4, 3, 6 |
3 |
5 |
6 |
2 |
6, 8, 7 |
1 |
3 |
3 |
2 |
8, 7, 9 |
17, 16, 18, 15, 19 |
12, 11, 10 |
| FH-a |
2 |
5, 7, 6 |
3 |
6, 7 |
6 |
2 |
6, 7, 5 |
1 |
3 |
3 |
2 |
7, 6 |
15, 14, 16 |
12, 11 |
| 39443 |
2 |
5, 4 |
3 |
6 |
6 |
2 |
8, 7 |
1 |
3 |
3 |
2 |
9, 10, 8 |
19, 18, 20 |
10, 9 |
| 19294 |
2 |
4, 5, 3, 6 |
3 |
5, 6 |
6 |
2 |
16, 17, 15, 18, 14, 8, 12, 13, 19, 11 |
1 |
3 |
3 |
2 |
11, 10, 12 |
19, 18, 20, 17 |
14, 13, 15, 12 |
| 3896 | 2d | 5, 4 | 3 | 5 | 8 | 2 | 10, 9, 11 | 1 | 3 | 3 | 2 | 11, 10, 9, 12, 8 | 17, 16, 15, 18, 19 | 10 |
†Based on references as detailed in Supplementary Table 1.
‡Determined based on NGS reads, except for those underlined which were determined using assembled contigs [7]. For loci containing variable numbers of repeats, the copy number is listed in the order from predominant to minor.
§Isolate FH-b is shown in the Supplementary Table 11 but not here since its NGS reads are too short to cover the repeat regions in most of the VNTR loci.
NGS: Next-generation sequencing; VNTR: Variable-number tandem repeat.