# cgMLST cluster report from joined allele database

#### 2020-11-24 12:28:14

# Cluster report for cluster CT_0004

## Basic information

This is a report for a single cluster

- Cluster name CT_0004

- Related external names are EpiCluster_1

- Serotype/clade information Typhimurium

- Last update on 2020-11-24

- Latest sample in cluster is C_GMI15-001-D-: 2020-06-01 (date of analysis)

- Oldest sample in cluster is A_GMI15-001-D-: 2020-01-01 (date of analysis)

- Duration: 152

- Cluster samples originate from partnerA, partnerB, partnerC

- Cluster contains 3 samples

- The cluster can be divided into the following number of subclusters: at 3 allele differences:2

## Cluster stats

## Information about subclusters

Count of subcluster members for samples clustered at 3 allele differences.

subcluster | n
--- | ---
Beta | 2

Note that sub-clusters containing only a single sample are omitted here.

## Provided samples per date

## Distance matrix

## single-linkage tree

    ## png
    ##   2

### Link to files

Overview of files found in folder, relative paths
name | file | Link
--- | --- | ---
cluster_information.tsv | cluster_information.tsv | cluster_information.tsv
clustering_tree.nwk | clustering_tree.nwk | clustering_tree.nwk
clustering_tree.png | clustering_tree.png | clustering_tree.png
clusterreport_files | clusterreport_files | clusterreport_files
distance_matrix.png | distance_matrix.png | distance_matrix.png
distance_matrix.tsv | distance_matrix.tsv | distance_matrix.tsv
mapping_sample2subclustername.tsv | mapping_sample2subclustername.tsv | mapping_sample2subclustername.tsv

### Subcluster details

### Color coding

The following color code is applied:

- partnerA
- partnerB
- partnerC

For the recency of samples, the color code is:

- Sample added in < 14 days
- Sample added in < 30 days
- Sample added in < 90 days
- no color (white) denotes samples added before 90 days

Furhermore, subclusters are marked in different colors.