SRR28267159 · 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 | 27.5946 |
| Chryseobacterium indologenes | Chryseobacterium | 24.0945 |
| Neisseria lactamica | Neisseria | 7.7437 |
| Campylobacter curvus | Campylobacter | 6.1461 |
| Neisseria dentiae | Neisseria | 5.9223 |
| Neisseria animalis | Neisseria | 4.8016 |
| Arcobacter trophiarum | Arcobacter | 3.6998 |
| Neisseria meningitidis | Neisseria | 2.0291 |
| Flavobacterium columnare | Flavobacterium | 1.9253 |
| Gallicola barnesae | Gallicola | 1.6414 |
| Arachidicoccus ginsenosidivorans | Arachidicoccus | 1.3220 |
| Campylobacter concisus | Campylobacter | 1.2592 |
| Flavobacterium frigidimaris | Flavobacterium | 1.1763 |
| Neisseria polysaccharea | Neisseria | 1.0825 |
| Flavobacterium hercynium | Flavobacterium | 1.0759 |
| Flavobacterium succinicans | Flavobacterium | 0.8133 |
| Chryseobacterium jeonii | Chryseobacterium | 0.7449 |
| Campylobacter fetus | Campylobacter | 0.7193 |
| Sphingobacterium multivorum | Sphingobacterium | 0.6662 |
| Sphingobacterium thalpophilum | Sphingobacterium | 0.6283 |
| Sphingobacterium mizutaii | Sphingobacterium | 0.6131 |
| Chryseobacterium balustinum | Chryseobacterium | 0.4733 |
| Neisseria zalophi | Neisseria | 0.4439 |
| Neisseria subflava | Neisseria | 0.4233 |
| Campylobacter helveticus | Campylobacter | 0.3644 |
| Kocuria rosea | Kocuria | 0.3335 |
| Parabacteroides merdae | Parabacteroides | 0.3252 |
| Flavobacterium flevense | Flavobacterium | 0.3119 |
| Mucilaginibacter polysacchareus | Mucilaginibacter | 0.3017 |
| Flavobacterium psychrophilum | Flavobacterium | 0.2959 |
| Parabacteroides goldsteinii | Parabacteroides | 0.2693 |
| Neisseria gonorrhoeae | Neisseria | 0.1957 |
| Massilia varians | Massilia | 0.1952 |
| Kocuria varians | Kocuria | 0.1899 |
| Novosphingobium aromaticivorans | Novosphingobium | 0.1774 |
Saved public metadata
{
"run_accession": "SRR28267159",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210668",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "87837",
"base_count": "143825403",
"fastq_bytes": "117656220",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/059/SRR28267159/SRR28267159_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": "b89169aadbcd63c632abfdd911ad03651e15e15c35ab0777b5301680a8970a5b",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1643.0,
"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": 8513,
"elapsed_seconds": 1.6018859679999977,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 106,
"fraction": 0.53,
"adapters_found": {
"RAP": 93,
"BC_FLANK": 6,
"27F": 7
},
"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."
}