SRR28257756 · Gut microbiome
SRR28257756
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 (%) |
|---|---|---|
| Escherichia coli | Escherichia | 60.8365 |
| Shigella dysenteriae | Shigella | 3.8097 |
| Lactococcus lactis | Lactococcus | 3.2428 |
| Clostridium perfringens | Clostridium | 3.1094 |
| Shigella sonnei | Shigella | 3.0999 |
| Escherichia fergusonii | Escherichia | 2.1598 |
| Clostridium botulinum | Clostridium | 2.1593 |
| Clostridium estertheticum | Clostridium | 2.0352 |
| Serratia marcescens | Serratia | 1.8407 |
| Helicobacter hepaticus | Helicobacter | 1.3218 |
| Helicobacter cholecystus | Helicobacter | 1.2227 |
| Clostridium thermosuccinogenes | Clostridium | 1.1978 |
| Clostridium phytofermentans | Clostridium | 1.0596 |
| Lactococcus garvieae | Lactococcus | 0.7242 |
| Clostridium beijerinckii | Clostridium | 0.6592 |
| Helicobacter canicola | Helicobacter | 0.6374 |
| Helicobacter mastomyrinus | Helicobacter | 0.6216 |
| Helicobacter typhlonius | Helicobacter | 0.6074 |
| Macrococcus caseolyticus | Macrococcus | 0.6041 |
| Shigella flexneri | Shigella | 0.5621 |
| Clostridium baratii | Clostridium | 0.5400 |
| Metamycoplasma hominis | Metamycoplasma | 0.5181 |
| Helicobacter pylori | Helicobacter | 0.4999 |
| Escherichia albertii | Escherichia | 0.4673 |
| Lactococcus taiwanensis | Lactococcus | 0.4571 |
| Malacoplasma penetrans | Malacoplasma | 0.4366 |
| Helicobacter bilis | Helicobacter | 0.4210 |
| Macrococcus canis | Macrococcus | 0.4114 |
| Serratia surfactantfaciens | Serratia | 0.3702 |
| Clostridium butyricum | Clostridium | 0.3666 |
| Mesomycoplasma flocculare | Mesomycoplasma | 0.3622 |
| Mesomycoplasma hyorhinis | Mesomycoplasma | 0.3551 |
| Helicobacter apodemus | Helicobacter | 0.3321 |
| Shigella boydii | Shigella | 0.3235 |
| Mesomycoplasma neurolyticum | Mesomycoplasma | 0.3154 |
| Malacoplasma iowae | Malacoplasma | 0.3113 |
| Serratia ficaria | Serratia | 0.2952 |
| Serratia plymuthica | Serratia | 0.2789 |
| Helicobacter macacae | Helicobacter | 0.2683 |
| Clostridium carnis | Clostridium | 0.2594 |
| Helicobacter fennelliae | Helicobacter | 0.2553 |
| Serratia rubidaea | Serratia | 0.2220 |
| Clostridium fallax | Clostridium | 0.2204 |
| Clostridium sporogenes | Clostridium | 0.2012 |
Saved public metadata
{
"run_accession": "SRR28257756",
"study_accession": "PRJNA1083214",
"sample_accession": "SAMN40240915",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "MinION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "135056",
"base_count": "211618192",
"fastq_bytes": "195749653",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR282/056/SRR28257756/SRR28257756_1.fastq.gz",
"sample_title": "",
"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": "f6dfb5df2b816852f05f155895943535733bb088312852c7f8035a54f9c629e2",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1592.0,
"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": 7218,
"elapsed_seconds": 6.499895801000093,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 12,
"fraction": 0.06,
"adapters_found": {
"BC_FLANK": 2,
"27F": 10
},
"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."
}