SRR28267089 · 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 (%) |
|---|---|---|
| Neisseria lactamica | Neisseria | 23.5972 |
| Neisseria dentiae | Neisseria | 22.9602 |
| Chryseobacterium indologenes | Chryseobacterium | 13.6230 |
| Neisseria animalis | Neisseria | 7.3218 |
| Campylobacter sputorum | Campylobacter | 5.6718 |
| Neisseria polysaccharea | Neisseria | 5.3183 |
| Neisseria meningitidis | Neisseria | 4.8143 |
| Arcobacter trophiarum | Arcobacter | 4.2605 |
| Campylobacter curvus | Campylobacter | 2.2993 |
| Neisseria subflava | Neisseria | 1.4506 |
| Granulicatella balaenopterae | Granulicatella | 1.2352 |
| Corynebacterium bovis | Corynebacterium | 0.5687 |
| Klebsiella variicola | Klebsiella | 0.5517 |
| Fusobacterium nucleatum | Fusobacterium | 0.5232 |
| Chryseobacterium balustinum | Chryseobacterium | 0.5168 |
| Neisseria zalophi | Neisseria | 0.4896 |
| Fusobacterium periodonticum | Fusobacterium | 0.4628 |
| Klebsiella pneumoniae | Klebsiella | 0.4087 |
| Neisseria arctica | Neisseria | 0.3610 |
| Granulicatella adiacens | Granulicatella | 0.3579 |
| Veillonella rodentium | Veillonella | 0.3430 |
| Neisseria gonorrhoeae | Neisseria | 0.3288 |
| Neisseria animaloris | Neisseria | 0.3084 |
| Corynebacterium matruchotii | Corynebacterium | 0.2788 |
| Parabacteroides merdae | Parabacteroides | 0.2744 |
| Kocuria rosea | Kocuria | 0.2640 |
| Neisseria dumasiana | Neisseria | 0.2363 |
| Snodgrassella alvi | Snodgrassella | 0.2227 |
| Campylobacter helveticus | Campylobacter | 0.2154 |
| Neisseria zoodegmatis | Neisseria | 0.2103 |
| Arcobacter butzleri | Arcobacter | 0.2037 |
| Kocuria varians | Kocuria | 0.1995 |
| Pseudomonas aeruginosa | Pseudomonas | 0.1220 |
Saved public metadata
{
"run_accession": "SRR28267089",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210557",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "158758",
"base_count": "261024121",
"fastq_bytes": "196529431",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/089/SRR28267089/SRR28267089_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": "db8e87117d35b3185d8359e724bfc5665a2bf8f0444c52752d5a998c1fb435f4",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1651.0,
"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": 6669,
"elapsed_seconds": 1.8722439440002745,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 109,
"fraction": 0.545,
"adapters_found": {
"RAP": 94,
"BC_FLANK": 15
},
"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."
}