MIMARKS Survey related sample from human oral metagenome
BioSample: SAMN40434846 · Study: PRJNA1087153 · Body site: not applicable
Interactive report · NCBI SRA · ENA
Relative abundance is normalized among reported taxa. No reported taxa does not establish absence of organisms.
| Species | Genus | Phylum | Abundance |
|---|
0 of 0 reported species have an eligible reference. MAFFT alignment and FastTree GTR+CAT tree, pruned to this sample. This is not a phylogeny inferred from sample reads or ASVs. Root placement is arbitrary; branch lengths are substitutions per site.
No eligible reference tips for this sample.
Files contain the original full run. Downloads are hosted by ENA.
| File | Type / bytes | MD5 |
|---|---|---|
| SRR28328439_1.fastq.gz | FASTQ / 2615 | 8268fa11d5a21b6d8beaaf57d43e2f95 |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 053ca4585b1429b3b6a0cbf218c4ffae66cf4af6a411907003685c2b7ba07974 |
| median_read_length | 228.0 |
| reads_in_length_window | 1 |
| length_window_bp | [1200, 2000] |
| quality_scores | Unavailable in fetched FASTA; no measured quality filtering |
| classifier_stats | {"marker": "16s", "pipeline": "v18.8", "gpu": "RTX-PRO-6000", "input_path": "volume-fastq-gz", "reads_in": 6, "reads_skipped": 6, "elapsed_seconds": 0.27650547400003234, "reads_submitted": 6, "reads_after_filter": 6, "adapter_scan": {"sampled": 6, "matched": 1, "fraction": 0.1667, "adapters_found": {"RAP": 1}, "should_trim": true}, "porechop_ran": false, "porechop_reason": "fast-path: no adapter trimming required"} |
All retrieved values are included. Blank source values are displayed as “Not reported”. Expand the sections below to inspect the full record.
| run_accession | SRR28328439 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | Not reported |
| bam_bytes | Not reported |
| bam_file_role | Not reported |
| bam_ftp | Not reported |
| bam_galaxy | Not reported |
| bam_md5 | Not reported |
| base_count | 2411 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | Not reported |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | SUB13973801 |
| checklist | Not reported |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2022 |
| collection_date_end | 2022-12-31 |
| collection_date_start | 2022-01-01 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Uganda:Kampala |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | MinION sequencing: DNA of Homo Sapiens: Saliva |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | Not reported |
| environment_biome | Not reported |
| environment_feature | Not reported |
| environment_material | Not reported |
| environmental_medium | Not reported |
| environmental_sample | Not reported |
| experiment_accession | SRX23936861 |
| experiment_alias | d29 |
| experiment_target | Not reported |
| experiment_title | MinION sequencing: DNA of Homo Sapiens: Saliva |
| experimental_factor | Not reported |
| experimental_protocol | Not reported |
| extraction_protocol | Not reported |
| faang_library_selection | Not reported |
| fastq_aspera | fasp.sra.ebi.ac.uk:/vol1/fastq/SRR283/039/SRR28328439/SRR28328439_1.fastq.gz |
| fastq_bytes | 2615 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/039/SRR28328439/SRR28328439_1.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/039/SRR28328439/SRR28328439_1.fastq.gz |
| fastq_md5 | 8268fa11d5a21b6d8beaaf57d43e2f95 |
| file_location | Not reported |
| first_created | 2024-03-19 |
| first_public | 2024-03-19 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Homo sapiens |
| host_body_site | Not reported |
| host_genotype | Not reported |
| host_gravidity | Not reported |
| host_growth_conditions | Not reported |
| host_phenotype | Not reported |
| host_scientific_name | Homo sapiens |
| host_sex | Not reported |
| host_status | Not reported |
| host_tax_id | 9606 |
| identified_by | Not reported |
| instrument_model | MinION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | saliva |
| last_updated | 2024-03-19 |
| lat | Not reported |
| library_construction_protocol | Not reported |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | d29 |
| library_pcr_isolation_protocol | Not reported |
| library_prep_date | Not reported |
| library_prep_date_format | Not reported |
| library_prep_latitude | Not reported |
| library_prep_location | Not reported |
| library_prep_longitude | Not reported |
| library_selection | PCR |
| library_source | METAGENOMIC |
| library_strategy | AMPLICON |
| local_environmental_context | Not reported |
| location | Not reported |
| location_end | Not reported |
| location_start | Not reported |
| lon | Not reported |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | MIMARKS.survey;MIGS/MIMS/MIMARKS.human-oral |
| nominal_length | Not reported |
| nominal_sdev | Not reported |
| pcr_isolation_protocol | Not reported |
| ph | Not reported |
| project_name | Not reported |
| protocol_label | Not reported |
| read_count | 6 |
| read_strand | Not reported |
| restriction_enzyme | Not reported |
| restriction_enzyme_target_sequence | Not reported |
| restriction_site | Not reported |
| rna_integrity_num | Not reported |
| rna_prep_3_protocol | Not reported |
| rna_prep_5_protocol | Not reported |
| rna_purity_230_ratio | Not reported |
| rna_purity_280_ratio | Not reported |
| rt_prep_protocol | Not reported |
| run_alias | d29a.fastq |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMN40434846 |
| sample_alias | e26a |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | d29 |
| sample_material | Not reported |
| sample_prep_interval | Not reported |
| sample_prep_interval_units | Not reported |
| sample_storage | Not reported |
| sample_storage_processing | Not reported |
| sample_title | MIMARKS Survey related sample from human oral metagenome |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | SRS20740542 |
| secondary_study_accession | SRP494951 |
| sequencing_date | Not reported |
| sequencing_date_format | Not reported |
| sequencing_location | Not reported |
| sequencing_longitude | Not reported |
| sequencing_method | Not reported |
| sequencing_primer_catalog | Not reported |
| sequencing_primer_lot | Not reported |
| sequencing_primer_provider | Not reported |
| serotype | Not reported |
| serovar | Not reported |
| sex | Not reported |
| specimen_voucher | Not reported |
| sra_aspera | Not reported |
| sra_bytes | Not reported |
| sra_file_role | Not reported |
| sra_ftp | Not reported |
| sra_galaxy | Not reported |
| sra_md5 | Not reported |
| status | public |
| strain | Not reported |
| study_accession | PRJNA1087153 |
| study_alias | PRJNA1087153 |
| study_title | sequencing data for a comparison of oral bacteriome associated with periodontal pockets for patients with and without diabetes mellitus in Uganda. |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | SRA1823377 |
| submission_tool | Not reported |
| submitted_aspera | Not reported |
| submitted_bytes | Not reported |
| submitted_file_role | Not reported |
| submitted_format | Not reported |
| submitted_ftp | Not reported |
| submitted_galaxy | Not reported |
| submitted_host_sex | Not reported |
| submitted_md5 | Not reported |
| submitted_read_type | Not reported |
| surveillance_target | Not reported |
| tag | Not reported |
| target_gene | Not reported |
| tax_id | 447426 |
| tax_lineage | 1;2787823;12908;408169;410656;447426 |
| taxonomic_classification | Not reported |
| taxonomic_identity_marker | Not reported |
| temperature | Not reported |
| tissue_lib | Not reported |
| tissue_type | Not reported |
| transposase_protocol | Not reported |
| variety | Not reported |
| alias | e26a |
|---|---|
| title | MIMARKS Survey related sample from human oral metagenome |
| description | d29 |
| collection_date | 2022 |
|---|---|
| INSDC secondary accession | SRS20740542 |
| organism | human oral metagenome |
| env_broad_scale | not applicable |
| sample_type | tissue_sample |
| env_local_scale | not applicable |
| NCBI submission package | MIMARKS.survey.human-oral.6.0 |
| library_ID | d29 |
| host | Homo sapiens |
| geo_loc_name | Uganda:Kampala |
| env_medium | not applicable |
| lat_lon | not collected |
| isolation_source | saliva |
| BioSampleModel | MIGS/MIMS/MIMARKS.human-oral |
| ENA-FIRST-PUBLIC | 2024-03-18 |
| ENA-LAST-UPDATE | 2024-03-18 |
| run | SRR28328439 |
|---|---|
| sample | SAMN40434846 |
| study | PRJNA1087153 |
| title | MIMARKS Survey related sample from human oral metagenome |
| alias | e26a |
| site | not applicable |
| subject | Not reported |
| phenotype | Not reported |
| sex | Not reported |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 6 |
| species_reported | 0 |
| human_primary | False |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.