SRR28267249 · 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 (%) |
|---|---|---|
| Klebsiella pneumoniae | Klebsiella | 38.1715 |
| Klebsiella variicola | Klebsiella | 32.4846 |
| Citrobacter europaeus | Citrobacter | 6.4817 |
| Citrobacter freundii | Citrobacter | 5.0139 |
| Neisseria dentiae | Neisseria | 3.3374 |
| Neisseria lactamica | Neisseria | 2.1495 |
| Campylobacter sputorum | Campylobacter | 1.4248 |
| Neisseria polysaccharea | Neisseria | 1.2173 |
| Neisseria animalis | Neisseria | 1.0891 |
| Chryseobacterium indologenes | Chryseobacterium | 0.9106 |
| Klebsiella aerogenes | Klebsiella | 0.7230 |
| Neisseria subflava | Neisseria | 0.6438 |
| Neisseria meningitidis | Neisseria | 0.6297 |
| Citrobacter portucalensis | Citrobacter | 0.6198 |
| Corynebacterium bovis | Corynebacterium | 0.5618 |
| Propioniciclava sinopodophylli | Propioniciclava | 0.5231 |
| Lactococcus garvieae | Lactococcus | 0.4779 |
| Arachidicoccus ginsenosidivorans | Arachidicoccus | 0.4779 |
| Kocuria rosea | Kocuria | 0.4450 |
| Paracoccus aestuarii | Paracoccus | 0.3746 |
| Kocuria varians | Kocuria | 0.3364 |
| Campylobacter curvus | Campylobacter | 0.2801 |
| Klebsiella terrigena | Klebsiella | 0.2389 |
| Gallicola barnesae | Gallicola | 0.2260 |
| Granulicatella balaenopterae | Granulicatella | 0.2131 |
| Citrobacter werkmanii | Citrobacter | 0.1874 |
| Klebsiella michiganensis | Klebsiella | 0.1679 |
| Citrobacter pasteurii | Citrobacter | 0.1475 |
| Dysgonomonas macrotermitis | Dysgonomonas | 0.1227 |
| Massilia varians | Massilia | 0.1033 |
| Spirosoma spitsbergense | Spirosoma | 0.0775 |
| Mucilaginibacter polysacchareus | Mucilaginibacter | 0.0710 |
| Sphingomonas paucimobilis | Sphingomonas | 0.0710 |
Saved public metadata
{
"run_accession": "SRR28267249",
"study_accession": "PRJNA1082425",
"sample_accession": "SAMN40210535",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "GENOMIC",
"library_selection": "PCR",
"read_count": "441445",
"base_count": "731373255",
"fastq_bytes": "551794816",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/049/SRR28267249/SRR28267249_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": "94ec105b468faf715c1c0ca3478a98b8793b187a751661a32d6f4b182673bf18",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1666.0,
"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": 4325,
"elapsed_seconds": 2.2568205069999987,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 112,
"fraction": 0.56,
"adapters_found": {
"RAP": 104,
"BC_FLANK": 7,
"27F": 1
},
"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."
}