SRR15676143 · Gut microbiome
Metagenome of Mus musculus
complete
Gut analysis is paused. Unfinished samples are not negative results. This is a mixed-host collection, not a curated human-only cohort.
Open interactive sample report
Taxonomic abundances
| Species | Genus | Abundance (%) |
|---|---|---|
| Helicobacter apodemus | Helicobacter | 20.4513 |
| Helicobacter pylori | Helicobacter | 9.4574 |
| Helicobacter canicola | Helicobacter | 8.6561 |
| Lactobacillus psittaci | Lactobacillus | 6.9379 |
| Ligilactobacillus murinus | Ligilactobacillus | 6.7141 |
| Helicobacter fennelliae | Helicobacter | 6.5011 |
| Helicobacter apri | Helicobacter | 5.8329 |
| Ligilactobacillus salivarius | Ligilactobacillus | 4.7375 |
| Lactobacillus johnsonii | Lactobacillus | 4.6122 |
| Helicobacter mastomyrinus | Helicobacter | 4.4603 |
| Helicobacter typhlonius | Helicobacter | 2.9849 |
| Limosilactobacillus reuteri | Limosilactobacillus | 2.5809 |
| Mucispirillum schaedleri | Mucispirillum | 2.0572 |
| Helicobacter acinonychis | Helicobacter | 1.7061 |
| Helicobacter macacae | Helicobacter | 1.6520 |
| Helicobacter bilis | Helicobacter | 1.2807 |
| Helicobacter hepaticus | Helicobacter | 1.2483 |
| Lactobacillus delbrueckii | Lactobacillus | 1.1035 |
| Ligilactobacillus saerimneri | Ligilactobacillus | 1.0188 |
| Helicobacter cholecystus | Helicobacter | 0.8805 |
| Ligilactobacillus agilis | Ligilactobacillus | 0.8786 |
| Ligilactobacillus acidipiscis | Ligilactobacillus | 0.7150 |
| Helicobacter pullorum | Helicobacter | 0.6695 |
| Lactobacillus gasseri | Lactobacillus | 0.6007 |
| Limosilactobacillus oris | Limosilactobacillus | 0.5424 |
| Helicobacter pametensis | Helicobacter | 0.4440 |
| Lactobacillus jensenii | Lactobacillus | 0.4439 |
| Helicobacter cetorum | Helicobacter | 0.4292 |
| Lactobacillus helveticus | Lactobacillus | 0.4032 |
Saved public metadata
{
"run_accession": "SRR15676143",
"study_accession": "PRJNA759117",
"sample_accession": "SAMN21156604",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "178340",
"base_count": "290566302",
"fastq_bytes": "306104798",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR156/043/SRR15676143/SRR15676143_1.fastq.gz",
"sample_title": "Metagenome of Mus musculus",
"scientific_name": "gut metagenome"
}Public files
Analysis provenance
{
"marker": "16S",
"pipeline": "Archaions v18.8",
"cohort": "Gut, mixed hosts; not curated as a human-only cohort",
"execution_state": "paused_by_user",
"sample_state": "complete",
"read_sampling": "First available reads; not random subsampling",
"input_sha256": "09f66324bf9bde113b30387f43412baf9d6b9156bb5f4ab220ed131d4e9b9a77",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1577.0,
"quality_scores": "No measured quality scores in fetched FASTA",
"classifier_stats": {
"marker": "16s",
"pipeline": "v18.8",
"gpu": "RTX-PRO-6000",
"input_path": "volume-fastq-gz",
"reads_in": 20000,
"reads_skipped": 14631,
"elapsed_seconds": 1.6218800589999773,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 2,
"fraction": 0.01,
"adapters_found": {
"27F": 2
},
"should_trim": false
},
"porechop_ran": false,
"porechop_reason": "fast-path: no adapter trimming required"
},
"metadata_coverage": "Saved ENA run fields only. BioSample attributes, study abstracts and file MD5s have not been fetched for this panel."
}