SRR13402263 · Gut microbiome
MIMARKS Survey related 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 (%) |
|---|---|---|
| Massilia varians | Massilia | 62.7727 |
| Massilia niastensis | Massilia | 4.7385 |
| Massilia oculi | Massilia | 3.9305 |
| Methylobacterium aerolatum | Methylobacterium | 3.6995 |
| Massilia albidiflava | Massilia | 3.2122 |
| Massilia violacea | Massilia | 3.1845 |
| Massilia niabensis | Massilia | 2.9837 |
| Massilia flava | Massilia | 1.4455 |
| Massilia suwonensis | Massilia | 1.4439 |
| Massilia jejuensis | Massilia | 1.2931 |
| Methylobacterium indicum | Methylobacterium | 1.0951 |
| Methylobacterium thuringiense | Methylobacterium | 1.0457 |
| Massilia umbonata | Massilia | 0.9823 |
| Massilia putida | Massilia | 0.9757 |
| Massilia haematophila | Massilia | 0.8994 |
| Massilia aerilata | Massilia | 0.8881 |
| Cutibacterium acnes | Cutibacterium | 0.8296 |
| Massilia armeniaca | Massilia | 0.8255 |
| Methylobacterium radiotolerans | Methylobacterium | 0.8132 |
| Massilia glaciei | Massilia | 0.7295 |
| Massilia kyonggiensis | Massilia | 0.5135 |
| Massilia consociata | Massilia | 0.5012 |
| Methylobacterium terrae | Methylobacterium | 0.4148 |
| Massilia plicata | Massilia | 0.4104 |
| Massilia psychrophila | Massilia | 0.3720 |
Saved public metadata
{
"run_accession": "SRR13402263",
"study_accession": "PRJNA691201",
"sample_accession": "SAMN17283452",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "21155",
"base_count": "25243423",
"fastq_bytes": "23005349",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR134/063/SRR13402263/SRR13402263_1.fastq.gz",
"sample_title": "MIMARKS Survey related 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": "4872bbe5b8984019a9bdbe38374aeaa35b4978b706c220bb2ab98f11cb006d8a",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1621.0,
"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": 13965,
"elapsed_seconds": 1.4994199289999983,
"reads_submitted": 20000,
"reads_after_filter": 20000,
"adapter_scan": {
"sampled": 200,
"matched": 17,
"fraction": 0.085,
"adapters_found": {
"1492R_rc": 5,
"27F": 12
},
"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."
}