SRR28267088 · 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 (%) |
|---|---|---|
| Chryseobacterium indologenes | Chryseobacterium | 21.1425 |
| Neisseria lactamica | Neisseria | 15.9039 |
| Neisseria dentiae | Neisseria | 12.5685 |
| Campylobacter sputorum | Campylobacter | 8.3115 |
| Neisseria animalis | Neisseria | 7.3304 |
| Arcobacter trophiarum | Arcobacter | 6.0778 |
| Neisseria polysaccharea | Neisseria | 3.6426 |
| Neisseria meningitidis | Neisseria | 3.1638 |
| Kocuria rosea | Kocuria | 2.1967 |
| Campylobacter curvus | Campylobacter | 1.9532 |
| Kocuria varians | Kocuria | 1.9340 |
| Dysgonomonas macrotermitis | Dysgonomonas | 1.7635 |
| Chryseobacterium balustinum | Chryseobacterium | 1.6742 |
| Ottowia pentelensis | Ottowia | 1.4634 |
| Neisseria subflava | Neisseria | 1.1892 |
| Gallicola barnesae | Gallicola | 1.1832 |
| Neisseria zalophi | Neisseria | 1.0915 |
| Lysobacter panacisoli | Lysobacter | 1.0379 |
| Arachidicoccus ginsenosidivorans | Arachidicoccus | 0.7992 |
| Allofrancisella guangzhouensis | Allofrancisella | 0.5647 |
| Dysgonomonas capnocytophagoides | Dysgonomonas | 0.5440 |
| Chryseobacterium indoltheticum | Chryseobacterium | 0.5225 |
| Chryseobacterium jeonii | Chryseobacterium | 0.4699 |
| Propioniciclava sinopodophylli | Propioniciclava | 0.4255 |
| Dietzia maris | Dietzia | 0.3529 |
| Dysgonomonas oryzarvi | Dysgonomonas | 0.3391 |
| Campylobacter concisus | Campylobacter | 0.3321 |
| Allofrancisella frigidaquae | Allofrancisella | 0.3321 |
| Neisseria gonorrhoeae | Neisseria | 0.2882 |
| Snodgrassella alvi | Snodgrassella | 0.2878 |
| Neisseria animaloris | Neisseria | 0.2770 |
| Campylobacter fetus | Campylobacter | 0.2698 |
| Klebsiella variicola | Klebsiella | 0.2180 |
| Neisseria arctica | Neisseria | 0.2144 |
| Mucilaginibacter polysacchareus | Mucilaginibacter | 0.1349 |
Saved public metadata
{
"run_accession": "SRR28267088",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210558",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "103874",
"base_count": "170720077",
"fastq_bytes": "139001368",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/088/SRR28267088/SRR28267088_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": "b1034348a6ddeed8635d45f9a9c2e3c0bb63e14c406d5bf324abcf66cf18e7ff",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1649.0,
"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": 10235,
"elapsed_seconds": 1.6612584219997188,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 103,
"fraction": 0.515,
"adapters_found": {
"RAP": 86,
"BC_FLANK": 12,
"27F": 5
},
"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."
}