Clicking the ‘Analysis’ tab produces a blank window and an ‘Analysis
Panel’ with the ability to select the definition used to divide the STs
into groups of related STs. The default setting is the sharing of alleles at
≥ 6 of the 7 loci with at least one other ST in the group (see previous).
Clicking the ‘Compute’ button
produces a display of the eBURST groups.
For each group, the group number is shown,
and the total number of isolates and STs
in the group, and the predicted primary
founder, if one can be assigned. Below
this, all the STs in the group are shown,
with the number of isolates of each ST
in the input data (frequency), the number
of STs in the group that differ at a single
locus (SLVs), those that differ at two
loci (DLVs), and at three loci (TLVs),
and those that are more distantly related
(satellites). Some STs may not share alleles
at six out of seven loci (or five out
of seven loci using the more relaxed group
definition) with any other STs in the
dataset and are shown at the bottom of
the tabular output, below all the groups,
as ‘singleton STs’.
The average distance of each ST to each other ST in the group is also shown,
and is computed from the average number of differences in their allelic profiles.
Thus, in a simple eBURST group (e.g. that shown in Table 1), where all STs
are SLVs of the primary founder, the average distance of the primary founder
will be 1.0 as all other STs differ from the founder at only a single locus.
The ST with the minimum average distance to other STs is likely to be the primary
founder and this measure provides another indicator of the likelihood of a
ST being the primary founder.
Table 1. Output for an eBURST group.
Group 7: No. Isolates = 20 | No. STs = 9 | Predicted
Founder = 354
ST FREQ SLV DLV TLV SAT Distance Group Subgrp
354 12 8 0 0 0 1.0 100% 100%
7 1 2 6 0 0 1.75 0% 0%
339 1 2 6 0 0 1.75 0% 0%
326 1 2 6 0 0 1.75 0% 0%
774 1 2 6 0 0 1.75 0% 0%
310 1 1 7 0 0 1.87 0% 0%
359 1 1 7 0 0 1.87 0% 0%
412 1 1 7 0 0 1.87 0% 0%
528 1 1 7 0 0 1.87 0% 0%
conditional bootstraps are calculated
for each ST being the primary founder
of the group and, with the default setting,
are displayed for re-samplings from
an initial dataset that contains only
one example of each ST in the input
data (ST Bootstrap in the above table).
Bootstrap values for re-samplings that
use all isolates in the input data (which
will typically include multiple isolates
of some STs) can be selected in the ‘Analysis
Menu’. Bootstrap support is only
provided with the default group setting,
where all isolates in the group are
considered to be members of a single
Bootstrap support is also shown for each ST being a subgroup founder. These
conditional bootstraps evaluate the number of times in the resampled datasets
each ST is associated with the required number of SLVs to be defined as a
subgroup founder. The default value for a subgroup founder is that it has
at least two descendent SLVs, but this value can be increased (using the
Analysis Panel), with corresponding changes in the level of bootstrap support
as a subgroup founder. Thus, bootstrap support for a ST as a subgroup founder
may be very high with the default definition but will decrease as the number
of STs that are required to define a subgroup increases.
The number of bootstrap re-samplings
can be changed from the default value
of 1000 in the ‘Analysis Panel’.
Bootstraps take a few seconds to appear
and the progress of the bootstrap calculations
can be followed in the ‘Analysis
Should you wish to know the group that
a particular ST falls into, a search
box is located in the ‘Analysis
Panel’ allowing you to enter an
ST number and click ‘Search’.
The query ST is shown highlighted in