Overview
The procedure statistics are automatically calculated by SeqSphere+. They are shown in the Procedure tab of the Sample Overview and they can be exported like epidemiological field data. The read and assembly procedure statistics can also be exported to and imported from SPEC Files.
Read Statistics
| Field | Description | Submission |
|---|---|---|
| Avg. Coverage (Unassembled)1) | Estimated based on the genome size of the reference genome and unprocessed reads | 
|
| Avg. Coverage (Processed, Unassembled)1) | Estimated based on the genome size of the reference genome and processed (trimming and/or downsampling) reads | |
| Avg. Read Length (Unassembled)1) | Average read length for unassambled reads |
|
| Avg. Read Length (Processed, Unassembled)1) | Average read length for processed (trimming and/or downsampling) and unassambled reads |
|
| Read Count (Unassembled)1) | Number of reads for unassambled reads | |
| Read Count (Processed, Unassembled)1) | Number of reads for processed (trimming and/or downsampling) and unassambled reads | |
| Read Base Count (Unassembled)1) | Sum of all read bases for unassambled reads | |
| Read Base Count (Processed, Unassembled)1) | Sum of all read bases for processed (trimming and/or downsampling) and unassambled reads |
1) only available if assembled with a SeqSphere+ pipeline
Potentially this field is submitted and published on cgMLST.org when the Sample is submitted.
Assembly Statistics
| Field | Description | Submission |
|---|---|---|
| Contig Count (Assembled) | Number of contigs in the assembly2) |
|
| N50 | N50 calculated for the assembly2) |
|
| Read Count (Assembled)3) | Number of reads used in the assembly | |
| Read Fwd Count (Assembled)3) | Number of forward reads used in the assembly | |
| Read Rev Count (Assembled)3) | Number of reverse reads used in the assembly | |
| Consensus Base Base Count (Assembled) | Number of bases in the assembly |
|
| Max Contig Length (Assembled) | Maximum length of a contig in the assembly2) | |
| Min Contig Length (Assembled) | Minimum length of a contig in the assembly2) | |
| Mean Contig Length (Assembled) | Mean length of a contig in the assembly2) | |
| Avg. Coverage (Assembled)4) | Estimated based on the consensus base count and assembled read base count, or imported from GenBank entry |
|
| Genome Status | Filled if the sequence data was imported from NCBI |
|
2) includes all contigs, i.e., also contigs that are smaller than 200 bases
3) only available if imported from ACE/BAM or assembled with a SeqSphere+ pipeline
4) only available if imported from ACE/BAM, assembled with a SeqSphere+ pipeline or available in GenBank entry
Potentially this field is submitted and published on cgMLST.org when the Sample is submitted.
cgMLST Statistics
| Field | Description | Submission |
|---|---|---|
| Procedure cgMLST Perc. Good Targets | Number of cgMLST targets that passed the initial target QC procedure | 
|
This field is submitted and published on cgMLST.org when the Sample is submitted.