SRR22537688 · Gut microbiome
WMF03
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 fennelliae | Helicobacter | 36.4259 |
| Helicobacter macacae | Helicobacter | 22.5397 |
| Campylobacter avium | Campylobacter | 5.6292 |
| Brachyspira intermedia | Brachyspira | 4.1077 |
| Helicobacter brantae | Helicobacter | 3.0094 |
| Helicobacter acinonychis | Helicobacter | 2.8303 |
| Helicobacter aurati | Helicobacter | 2.4181 |
| Helicobacter cholecystus | Helicobacter | 2.0702 |
| Campylobacter helveticus | Campylobacter | 2.0406 |
| Helicobacter pametensis | Helicobacter | 2.0364 |
| Helicobacter hepaticus | Helicobacter | 1.5753 |
| Helicobacter apodemus | Helicobacter | 1.4728 |
| Brachyspira hyodysenteriae | Brachyspira | 1.4422 |
| Helicobacter bilis | Helicobacter | 1.4380 |
| Helicobacter pylori | Helicobacter | 1.3674 |
| Anaerococcus vaginalis | Anaerococcus | 1.1251 |
| Brachyspira innocens | Brachyspira | 0.8793 |
| Helicobacter typhlonius | Helicobacter | 0.8611 |
| Campylobacter troglodytis | Campylobacter | 0.7540 |
| Lactobacillus johnsonii | Lactobacillus | 0.7449 |
| Campylobacter hyointestinalis | Campylobacter | 0.6727 |
| Arcanobacterium haemolyticum | Arcanobacterium | 0.5858 |
| Campylobacter lari | Campylobacter | 0.5715 |
| Porphyromonas levii | Porphyromonas | 0.5641 |
| Prevotella buccalis | Prevotella | 0.4774 |
| Campylobacter jejuni | Campylobacter | 0.3330 |
| Helicobacter pullorum | Helicobacter | 0.3197 |
| Brachyspira pilosicoli | Brachyspira | 0.3184 |
| Prevotella copri | Prevotella | 0.3110 |
| Campylobacter cuniculorum | Campylobacter | 0.2206 |
| Anaerococcus jeddahensis | Anaerococcus | 0.2056 |
| Brachyspira aalborgi | Brachyspira | 0.1809 |
| Campylobacter upsaliensis | Campylobacter | 0.1679 |
| Limosilactobacillus reuteri | Limosilactobacillus | 0.1519 |
| Porphyromonas bennonis | Porphyromonas | 0.1519 |
Saved public metadata
{
"run_accession": "SRR22537688",
"study_accession": "PRJNA908263",
"sample_accession": "SAMN32033828",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "OTHER",
"library_selection": "PCR",
"read_count": "18606",
"base_count": "22441049",
"fastq_bytes": "17429432",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR225/088/SRR22537688/SRR22537688_1.fastq.gz",
"sample_title": "WMF03",
"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": "2e8e455e93c5108d9f3c6d43d434c0553c297a295aa76d47a6d033ab648f477f",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1456.0,
"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": 18606,
"reads_skipped": 4688,
"elapsed_seconds": 1.720274720999896,
"reads_submitted": 18606,
"reads_after_filter": 18606,
"adapter_scan": {
"sampled": 200,
"matched": 0,
"fraction": 0.0,
"adapters_found": {},
"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."
}