SRR28267250 · 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 (%) |
|---|---|---|
| Kocuria rosea | Kocuria | 19.8984 |
| Kocuria varians | Kocuria | 12.4130 |
| Neisseria lactamica | Neisseria | 10.5106 |
| Neisseria dentiae | Neisseria | 9.6445 |
| Gallicola barnesae | Gallicola | 9.1888 |
| Neisseria animalis | Neisseria | 4.6350 |
| Neisseria polysaccharea | Neisseria | 4.5157 |
| Campylobacter sputorum | Campylobacter | 3.5669 |
| Neisseria meningitidis | Neisseria | 2.9876 |
| Arcobacter trophiarum | Arcobacter | 2.9083 |
| Enterococcus faecium | Enterococcus | 2.6027 |
| Kocuria rhizophila | Kocuria | 1.5858 |
| Neisseria subflava | Neisseria | 1.3702 |
| Fusobacterium nucleatum | Fusobacterium | 1.1465 |
| Propioniciclava sinopodophylli | Propioniciclava | 1.1438 |
| Fusobacterium periodonticum | Fusobacterium | 1.1004 |
| Kocuria indica | Kocuria | 1.0757 |
| Dysgonomonas macrotermitis | Dysgonomonas | 0.9837 |
| Campylobacter curvus | Campylobacter | 0.9349 |
| Kocuria subflava | Kocuria | 0.8680 |
| Tessaracoccus flavus | Tessaracoccus | 0.6596 |
| Neisseria zalophi | Neisseria | 0.6294 |
| Propioniciclava tarda | Propioniciclava | 0.6268 |
| Neisseria animaloris | Neisseria | 0.5826 |
| Granulicatella balaenopterae | Granulicatella | 0.5323 |
| Elizabethkingia miricola | Elizabethkingia | 0.4398 |
| Citrobacter freundii | Citrobacter | 0.4059 |
| Enterococcus alcedinis | Enterococcus | 0.3946 |
| Neisseria dumasiana | Neisseria | 0.3540 |
| Citrobacter europaeus | Citrobacter | 0.3463 |
| Campylobacter fetus | Campylobacter | 0.3356 |
| Fusobacterium ulcerans | Fusobacterium | 0.3299 |
| Neisseria zoodegmatis | Neisseria | 0.3218 |
| Microbacterium lindanitolerans | Microbacterium | 0.2892 |
| Fusobacterium hwasookii | Fusobacterium | 0.2665 |
| Exiguobacterium artemiae | Exiguobacterium | 0.2430 |
| Sphingomonas paucimobilis | Sphingomonas | 0.1620 |
Saved public metadata
{
"run_accession": "SRR28267250",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210534",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "39776",
"base_count": "64953786",
"fastq_bytes": "51356643",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/050/SRR28267250/SRR28267250_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": "9c6cd170c5e5e736f2335be939d7b93bb53f014a8cd6488ddd6079ed5e80ee20",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1644.0,
"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": 11130,
"elapsed_seconds": 1.5719403410002997,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 99,
"fraction": 0.495,
"adapters_found": {
"RAP": 84,
"BC_FLANK": 8,
"27F": 5,
"1492R_rc": 2
},
"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."
}