Table 1. Replicated isolates included as controls in the GBS analysis, and average genetic distances among replicates and within their respective lineages.
| Isolate namew | Genetic distance between replicatesx | DNA extraction #y | GBS run #z |
|---|---|---|---|
| Lineage US-23 | |||
| 11238_18 | 0.043 | 1 | 1 |
| 11238orgnl_90 | 1 | 2 | |
| 11238orgnl_93 | 1 | 3 | |
| 11238cntl1_88 | 2 | 2 | |
| 11238cntl1_91 | 2 | 3 | |
| 11238cntl2_89 | 3 | 2 | |
| 11238cntl2_92 | 3 | 3 | |
| 1726cntl22 | 0.042 | 1 | 3 |
| 1726cntl57 | 2 | 3 | |
| Average genetic distance among replicates: | 0.043 | ||
| Average genetic distance within entire lineage: | 0.089 | ||
| Lineage US-8 | |||
| 1301cntl01 | 0.048 | 1 | 1 |
| 1301cntl94 | 2 | 1 | |
| 1576cntlP2 | 0.088 | 1 | 2 |
| 1576cntlP3 | 2 | 3 | |
| 824cntlP1 | 0.054 | 1 | 1 |
| 824cntlP2 | 2 | 2 | |
| 2039cntlP1 | 0.085 | 1 | 1 |
| 2039cntlP2 | 2 | 2 | |
| Average genetic distance among replicates: | 0.069 | ||
| Average genetic distance within entire lineage: | 0.119 | ||
| Lineage US-11 | |||
| 1310cntlP1 | 0.066 | 1 | 1 |
| 1310cntlP2 | 2 | 2 | |
| 1403cntlP1 | 0.046 | 1 | 1 |
| 1403cntlP2 | 2 | 2 | |
| Average genetic distance among replicates: | 0.056 | ||
| Average genetic distance within entire lineage: | 0.095 | ||
w Isolate names beginning with the same 3 to 5 numbers are the same isolate, with the latter part of the isolate names identifying replicate information.
x Values are pairwise genetic distances (Prevosti’s distance) between pairs of replicated samples. The value for isolate 11238 is the average of all pairwise genetic distances between seven replicates of isolate 11238.
y Identical DNA extracts from the same isolate run as GBS replicates are indicated by the same DNA extraction number. Different DNA extracts from identical isolates are indicated by different DNA extraction numbers.
z The study included a total of three 96-well GBS runs. Replicated control samples were included in each of the three runs.