SRR28257773 · Gut microbiome
SRR28257773
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 (%) |
|---|---|---|
| Lactococcus lactis | Lactococcus | 24.1309 |
| Clostridium botulinum | Clostridium | 15.8263 |
| Clostridium perfringens | Clostridium | 7.3416 |
| Clostridium carnis | Clostridium | 6.5006 |
| Lactococcus garvieae | Lactococcus | 5.4437 |
| Clostridium estertheticum | Clostridium | 5.2832 |
| Lactococcus taiwanensis | Lactococcus | 4.7048 |
| Clostridium sporogenes | Clostridium | 4.2543 |
| Clostridium tetani | Clostridium | 3.5810 |
| Clostridium fallax | Clostridium | 3.0857 |
| Clostridium cochlearium | Clostridium | 3.0524 |
| Clostridium scatologenes | Clostridium | 1.7934 |
| Clostridium beijerinckii | Clostridium | 1.7489 |
| Clostridium baratii | Clostridium | 1.4422 |
| Clostridium butyricum | Clostridium | 1.3830 |
| Leuconostoc mesenteroides | Leuconostoc | 1.2763 |
| Clostridium septicum | Clostridium | 1.1709 |
| Leuconostoc lactis | Leuconostoc | 1.0515 |
| Clostridium psychrophilum | Clostridium | 0.7734 |
| Leuconostoc carnosum | Leuconostoc | 0.6647 |
| Clostridium phytofermentans | Clostridium | 0.5797 |
| Clostridium isatidis | Clostridium | 0.5662 |
| Lactococcus kimchii | Lactococcus | 0.5540 |
| Clostridium algoriphilum | Clostridium | 0.4823 |
| Clostridium ramosum | Clostridium | 0.4462 |
| Clostridium budayi | Clostridium | 0.3407 |
| Clostridium thermosuccinogenes | Clostridium | 0.3290 |
| Leuconostoc gelidum | Leuconostoc | 0.3060 |
| Clostridium saccharobutylicum | Clostridium | 0.2840 |
| Leuconostoc pseudomesenteroides | Leuconostoc | 0.2816 |
| Clostridium felsineum | Clostridium | 0.2699 |
| Lactococcus fujiensis | Lactococcus | 0.2577 |
| Clostridium polynesiense | Clostridium | 0.2314 |
| Lactococcus formosensis | Lactococcus | 0.2007 |
| Clostridium chromiireducens | Clostridium | 0.1841 |
| Clostridium pasteurianum | Clostridium | 0.1776 |
Saved public metadata
{
"run_accession": "SRR28257773",
"study_accession": "PRJNA1083214",
"sample_accession": "SAMN40240916",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "15620",
"base_count": "23189963",
"fastq_bytes": "21752654",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/073/SRR28257773/SRR28257773_1.fastq.gz",
"sample_title": "",
"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": "8b68eb46f0633491602ebb2e8a27f48e8ddbe1aea2e83b336477e2c07b94c8b8",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1538.0,
"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": 15620,
"reads_skipped": 2842,
"elapsed_seconds": 1.7769244119999712,
"reads_submitted": 15620,
"reads_after_filter": 15620,
"adapter_scan": {
"sampled": 200,
"matched": 29,
"fraction": 0.145,
"adapters_found": {
"27F": 29
},
"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."
}