Full information on isolate SRR7429574 (id:61509)
Projects
This isolate is a member of the following project:
- Public isolates
- Isolates publicly available for consultation
Provenance/primary metadata
- id
- 61509
- isolate
- SRR7429574
- alias
- RL15001419
- species
- L. monocytogenes
- sender
- Alexandra Moura, Institut Pasteur, France
- curator
- Auto Tagger
- update history
- 19 updates show details
- embargo history
- show details
- date entered
- 2020-11-27
- datestamp
- 2025-09-23
- isolation year
- 2010
- country
- Unknown
- source
- Human
- source description
- human
- phylogenetic lineage
- II
- clonal complex
- CC18
- sublineage
- SL18
- cgmlst type
- CT10212
- accession number
- SRR7429574
Publication (1)
- Painset A, Björkman JT, Kiil K, Guillier L, Mariet JF, Félix B, Amar C, Rotariu O, Roussel S, Perez-Reche F, Brisse S, Moura A, Lecuit M, Forbes K, Strachan N, Grant K, Møller-Nielsen E, Dallman TJ (2019). LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe. Microb Genom 5:
Sequence bin
- method
- Illumina
- contigs
- 22
- total length
- 2,873,603 bp
- max length
- 635,720 bp
- mean length
- 130,619 bp
- N50
- 516,692
- L50
- 3
- N90
- 64,121
- L90
- 8
- N95
- 47,281
- L95
- 10
- %GC
- 37.92
- Ns
- 0
- gaps
- 0
- loci tagged
- 3,583
Assembly checks
| Check | Status | Warn/fail reason |
|---|---|---|
| Number of contigs | ||
| Assembly size | ||
| Minimum N50 | ||
| %GC |
Similar isolates (determined by LIN codes)
- Scheme
- cgMLST1748_v2
- LIN code
- 0_0_0_0_3_0_2_0_0_0_0_0
- Lineage
- 0
- Sublineage
- SL18
- Genetic cluster
- GC15198
| Prefix | Threshold | Matching isolates |
|---|---|---|
| 0_0_0_0_3_0_2_0 | 7 | 1 |
| 0_0_0_0_3_0_2_0_0 | 4 | 1 |
| 0_0_0_0_3_0_2_0_0_0 | 2 | 1 |
| 0_0_0_0_3_0_2_0_0_0_0 | 1 | 1 |
| 0_0_0_0_3_0_2_0_0_0_0_0 | 0 | 1 |
| 0 | 1660 | 1995 |
| 0_0 | 1500 | 1993 |
| 0_0_0 | 1342 | 1982 |
| 0_0_0_0 | 1182 | 619 |
| 0_0_0_0_3 | 1020 | 20 |
| 0_0_0_0_3_0 | 200 | 20 |
| 0_0_0_0_3_0_2 | 50 | 1 |
| 0_0_0_0_3_0_2_0 | 7 | 1 |
| 0_0_0_0_3_0_2_0_0 | 4 | 1 |
| 0_0_0_0_3_0_2_0_0_0 | 2 | 1 |
| 0_0_0_0_3_0_2_0_0_0_0 | 1 | 1 |
| 0_0_0_0_3_0_2_0_0_0_0_0 | 0 | 1 |
Similar isolates (determined by classification schemes)
Some groups only contain this isolate. Show single groups
Experimental schemes are subject to change and are not a stable part of the nomenclature.
| Classification scheme | Underlying scheme | Clustering method | Mismatch threshold | Status | Group |
|---|---|---|---|---|---|
| auto_cgclust_150 | cgMLST1748 | Single-linkage | 150 | experimental | 327 (16 isolates) |
| auto_cgclust_500 | cgMLST1748 | Single-linkage | 500 | experimental | 20 (16 isolates) |
| auto_cgclust_1000 | cgMLST1748 | Single-linkage | 1000 | experimental | 19 (16 isolates) |
| auto_cgclust_1500 | cgMLST1748 | Single-linkage | 1500 | experimental | 2 (1334 isolates) |
| auto_cgclust_4 | cgMLST1748 | Single-linkage | 4 | experimental | 2827 (1 isolate) |
| auto_cgclust_7 | cgMLST1748 | Single-linkage | 7 | experimental | 2512 (1 isolate) |
| auto_cgclust_10 | cgMLST1748 | Single-linkage | 10 | experimental | 2252 (1 isolate) |
| auto_cgclust_30 | cgMLST1748 | Single-linkage | 30 | experimental | 759 (1 isolate) |
| auto_cgclust_150 | cgMLST1748 | Single-linkage | 150 | experimental | 327 (16 isolates) |
| auto_cgclust_500 | cgMLST1748 | Single-linkage | 500 | experimental | 20 (16 isolates) |
| auto_cgclust_1000 | cgMLST1748 | Single-linkage | 1000 | experimental | 19 (16 isolates) |
| auto_cgclust_1500 | cgMLST1748 | Single-linkage | 1500 | experimental | 2 (1334 isolates) |
Schemes and loci
Navigate and select schemes within tree to display allele designations
Tools
Export:
Analysis: