SRR28267142 · Gut microbiome
Metagenome or environmental sample from 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 (%) |
|---|---|---|
| Campylobacter sputorum | Campylobacter | 32.5881 |
| Campylobacter curvus | Campylobacter | 10.0757 |
| Neisseria lactamica | Neisseria | 6.6938 |
| Chryseobacterium indologenes | Chryseobacterium | 5.9627 |
| Kocuria varians | Kocuria | 5.5376 |
| Kocuria rosea | Kocuria | 5.3773 |
| Neisseria dentiae | Neisseria | 3.7262 |
| Bacteroides timonensis | Bacteroides | 3.2437 |
| Neisseria animalis | Neisseria | 3.0392 |
| Gallicola barnesae | Gallicola | 2.9077 |
| Clostridium thermosuccinogenes | Clostridium | 2.2511 |
| Campylobacter concisus | Campylobacter | 1.7846 |
| Propioniciclava sinopodophylli | Propioniciclava | 1.6875 |
| Neisseria meningitidis | Neisseria | 1.3716 |
| Arachidicoccus ginsenosidivorans | Arachidicoccus | 1.1658 |
| Paracoccus aestuarii | Paracoccus | 1.1249 |
| Campylobacter fetus | Campylobacter | 1.0829 |
| Parabacteroides merdae | Parabacteroides | 1.0720 |
| Paracoccus kondratievae | Paracoccus | 0.9788 |
| Corynebacterium bovis | Corynebacterium | 0.9625 |
| Nocardioides marmoraquaticus | Nocardioides | 0.8710 |
| Tessaracoccus aquimaris | Tessaracoccus | 0.8381 |
| Lactococcus garvieae | Lactococcus | 0.7236 |
| Propioniciclava tarda | Propioniciclava | 0.6306 |
| Corynebacterium ammoniagenes | Corynebacterium | 0.5793 |
| Tessaracoccus flavus | Tessaracoccus | 0.5554 |
| Kocuria rhizophila | Kocuria | 0.5416 |
| Neisseria polysaccharea | Neisseria | 0.4757 |
| Neisseria subflava | Neisseria | 0.4380 |
| Corynebacterium matruchotii | Corynebacterium | 0.4280 |
| Bacteroides stercoris | Bacteroides | 0.3742 |
| Kocuria subflava | Kocuria | 0.3082 |
| Brevundimonas bacteroides | Brevundimonas | 0.2814 |
| Acinetobacter baumannii | Acinetobacter | 0.1742 |
| Sphingomonas paucimobilis | Sphingomonas | 0.1474 |
Saved public metadata
{
"run_accession": "SRR28267142",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210549",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "84865",
"base_count": "139008372",
"fastq_bytes": "111881880",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/042/SRR28267142/SRR28267142_1.fastq.gz",
"sample_title": "Metagenome or environmental sample from 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": "c48b8bb3c4a056487d586beb548dc2d1aab42b71ec4107fab99c330f82b20ff6",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1645.0,
"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": 12250,
"elapsed_seconds": 1.6412766700004795,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 107,
"fraction": 0.535,
"adapters_found": {
"RAP": 99,
"27F": 2,
"BC_FLANK": 6
},
"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."
}