SRR13402258 · 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 | 53.1323 |
| Methylobacterium aerolatum | Methylobacterium | 4.2114 |
| Massilia niastensis | Massilia | 4.0137 |
| Massilia oculi | Massilia | 3.8366 |
| Massilia albidiflava | Massilia | 3.4223 |
| Bacillus amyloliquefaciens | Bacillus | 3.1259 |
| Massilia violacea | Massilia | 2.6340 |
| Massilia niabensis | Massilia | 2.2397 |
| Methylobacterium indicum | Methylobacterium | 1.8939 |
| Massilia umbonata | Massilia | 1.4897 |
| Massilia flava | Massilia | 1.4581 |
| Massilia suwonensis | Massilia | 1.2968 |
| Massilia jejuensis | Massilia | 1.2066 |
| Massilia putida | Massilia | 1.1172 |
| Cutibacterium acnes | Cutibacterium | 1.0578 |
| Bacillus velezensis | Bacillus | 1.0372 |
| Methylobacterium terrae | Methylobacterium | 1.0271 |
| Massilia haematophila | Massilia | 0.9996 |
| Massilia armeniaca | Massilia | 0.9646 |
| Methylobacterium radiotolerans | Methylobacterium | 0.8958 |
| Bacillus pumilus | Bacillus | 0.7679 |
| Massilia glaciei | Massilia | 0.7435 |
| Massilia aerilata | Massilia | 0.7403 |
| Massilia kyonggiensis | Massilia | 0.7387 |
| Methylobacterium thuringiense | Methylobacterium | 0.7269 |
| Methylobacterium phyllosphaerae | Methylobacterium | 0.6816 |
| Methylobacterium trifolii | Methylobacterium | 0.6441 |
| Methylobacterium iners | Methylobacterium | 0.5662 |
| Bacillus thuringiensis | Bacillus | 0.5629 |
| Methylobacterium oryzae | Methylobacterium | 0.5285 |
| Massilia plicata | Massilia | 0.5274 |
| Stenotrophomonas daejeonensis | Stenotrophomonas | 0.5119 |
| Massilia psychrophila | Massilia | 0.4932 |
| Massilia consociata | Massilia | 0.4506 |
| Actinopolyspora erythraea | Actinopolyspora | 0.2559 |
Saved public metadata
{
"run_accession": "SRR13402258",
"study_accession": "PRJNA691201",
"sample_accession": "SAMN17283457",
"instrument_platform": "OXFORD_NANOPORE",
"instrument_model": "GridION",
"library_strategy": "AMPLICON",
"library_source": "METAGENOMIC",
"library_selection": "PCR",
"read_count": "17846",
"base_count": "22687672",
"fastq_bytes": "20923656",
"fastq_ftp": "ftp.sra.ebi.ac.uk/vol1/fastq/SRR134/058/SRR13402258/SRR13402258_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": "41fb55684176da9f1a2830c53e26f13ee2b597ae0b95eda41be2ec44995e0470",
"length_window_bp": [
1200,
2000
],
"median_read_length": 1629.0,
"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": 17846,
"reads_skipped": 11964,
"elapsed_seconds": 1.5474646010000015,
"reads_submitted": 17846,
"reads_after_filter": 17846,
"adapter_scan": {
"sampled": 200,
"matched": 4,
"fraction": 0.02,
"adapters_found": {
"27F": 4
},
"should_trim": false
},
"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."
}