SRR18996186 · Gut microbiome
gut metagenome
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 (%) |
|---|---|---|
| Lonsdalea quercina | Lonsdalea | 15.4958 |
| Lonsdalea britannica | Lonsdalea | 15.1759 |
| Rahnella aquatilis | Rahnella | 8.8659 |
| Providencia rettgeri | Providencia | 8.2675 |
| Erwinia billingiae | Erwinia | 7.8146 |
| Lonsdalea populi | Lonsdalea | 7.4197 |
| Enterococcus faecium | Enterococcus | 6.5660 |
| Erwinia tracheiphila | Erwinia | 5.9072 |
| Providencia alcalifaciens | Providencia | 4.0400 |
| Erwinia amylovora | Erwinia | 2.1804 |
| Enterococcus columbae | Enterococcus | 1.7943 |
| Erwinia persicina | Erwinia | 1.6025 |
| Erwinia pyrifoliae | Erwinia | 1.5730 |
| Ignatzschineria indica | Ignatzschineria | 1.5544 |
| Macrococcus canis | Macrococcus | 1.2096 |
| Enterococcus faecalis | Enterococcus | 0.8692 |
| Malacoplasma iowae | Malacoplasma | 0.8322 |
| Macrococcus brunensis | Macrococcus | 0.8120 |
| Terriglobus albidus | Terriglobus | 0.6295 |
| Erwinia tasmaniensis | Erwinia | 0.5949 |
| Ignatzschineria ureiclastica | Ignatzschineria | 0.5814 |
| Rahnella inusitata | Rahnella | 0.5765 |
| Malacoplasma muris | Malacoplasma | 0.5167 |
| Macrococcus bovicus | Macrococcus | 0.4786 |
| Comamonas terrigena | Comamonas | 0.4272 |
| Enterococcus avium | Enterococcus | 0.4222 |
| Vagococcus teuberi | Vagococcus | 0.3726 |
| Macrococcus epidermidis | Macrococcus | 0.3580 |
| Macrococcus goetzii | Macrococcus | 0.3580 |
| Leuconostoc mesenteroides | Leuconostoc | 0.3548 |
| Vagococcus fluvialis | Vagococcus | 0.3486 |
| Macrococcus caseolyticus | Macrococcus | 0.3146 |
| Macrococcus equipercicus | Macrococcus | 0.2948 |
| Rahnella variigena | Rahnella | 0.2923 |
| Vagococcus penaei | Vagococcus | 0.2799 |
| Leuconostoc lactis | Leuconostoc | 0.2747 |
| Lonsdalea iberica | Lonsdalea | 0.2746 |
| Providencia thailandensis | Providencia | 0.2698 |
Saved public metadata
{
"run_accession": "SRR18996186",
"study_accession": "PRJNA827637",
"sample_accession": "SAMN27615865",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "81915",
"base_count": "121231470",
"fastq_bytes": "110239620",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR189/086/SRR18996186/SRR18996186_1.fastq.gz",
"sample_title": "gut metagenome",
"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": "b3e27d6c55aedc03482c2973babafb91eb3b5e40311f35e2c99e666f25c0da5d",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1482.0,
"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": 11075,
"elapsed_seconds": 1.6029730349998772,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 47,
"fraction": 0.235,
"adapters_found": {
"BC_FLANK": 43,
"27F": 4
},
"should_trim": true
},
"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."
}