15088.MRI1952DJAP065.B.16S
BioSample: SAMEA114596691 · Study: PRJEB68381 · Body site: buccal swab
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 |
|---|---|---|---|
| Haemophilus haemolyticus | Haemophilus | Pseudomonadota | 28.38628% |
| Haemophilus parainfluenzae | Haemophilus | Pseudomonadota | 15.15322% |
| Haemophilus influenzae | Haemophilus | Pseudomonadota | 10.45171% |
| Gemella haemolysans | Gemella | Bacillota | 9.90324% |
| Haemophilus aegyptius | Haemophilus | Pseudomonadota | 5.87707% |
| Streptococcus mitis | Streptococcus | Bacillota | 5.65261% |
| Streptococcus parasanguinis | Streptococcus | Bacillota | 4.59636% |
| Streptococcus salivarius | Streptococcus | Bacillota | 4.59427% |
| Gemella palaticanis | Gemella | Bacillota | 3.18783% |
| Streptococcus pneumoniae | Streptococcus | Bacillota | 1.74620% |
| Streptococcus downei | Streptococcus | Bacillota | 1.43953% |
| Veillonella parvula | Veillonella | Bacillota | 1.33999% |
| Streptococcus oralis | Streptococcus | Bacillota | 1.18241% |
| Veillonella dispar | Veillonella | Bacillota | 0.79777% |
| Haemophilus paraphrohaemolyticus | Haemophilus | Pseudomonadota | 0.66567% |
| Haemophilus haemoglobinophilus | Haemophilus | Pseudomonadota | 0.65011% |
| Streptococcus koreensis | Streptococcus | Bacillota | 0.63911% |
| Neisseria flavescens | Neisseria | Pseudomonadota | 0.60702% |
| Streptococcus sanguinis | Streptococcus | Bacillota | 0.57078% |
| Granulicatella adiacens | Granulicatella | Bacillota | 0.52784% |
| Haemophilus parahaemolyticus | Haemophilus | Pseudomonadota | 0.47489% |
| Haemophilus sputorum | Haemophilus | Pseudomonadota | 0.46827% |
| Streptococcus infantis | Streptococcus | Bacillota | 0.40230% |
| Streptococcus vestibularis | Streptococcus | Bacillota | 0.35823% |
| Streptococcus thermophilus | Streptococcus | Bacillota | 0.32728% |
25 of 25 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.
Files contain the original full run. Downloads are hosted by ENA.
| File | Type / bytes | MD5 |
|---|---|---|
| ERR12254126.fastq.gz | FASTQ / 346021890 | 26671502ec55080ffa754b583ca14e32 |
| 15088.MRI1952DJAP065.B.16S.R1.fastq.gz | Submitted file / 429350025 | 1b92ded78f1f808ae81ee5c97c778c8f |
| marker | 16S |
|---|---|
| pipeline | Archaions v18.8 |
| read_sampling | First available reads, not random subsampling |
| input_sha256 | 26e08952a32788c88c1b8a60c4d2ec6a8918690455e0711dec390d70b17963b1 |
| median_read_length | 1445.0 |
| reads_in_length_window | 7969 |
| 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": 10000, "reads_skipped": 2309, "elapsed_seconds": 1.027077423999998, "reads_submitted": 10000, "reads_after_filter": 10000, "adapter_scan": {"sampled": 200, "matched": 32, "fraction": 0.16, "adapters_found": {"BC_FLANK": 31, "27F": 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 | ERR12254126 |
|---|---|
| age | Not reported |
| aligned | Not reported |
| altitude | Not reported |
| assembly_quality | Not reported |
| assembly_software | Not reported |
| bam_aspera | fasp.sra.ebi.ac.uk:/vol1/err/ERR122/026/ERR12254126/ERR12254126.bam |
| bam_bytes | 358513489 |
| bam_file_role | ARCHIVAL_FILE |
| bam_ftp | ftp.sra.ebi.ac.uk/vol1/err/ERR122/026/ERR12254126/ERR12254126.bam |
| bam_galaxy | ftp.sra.ebi.ac.uk/vol1/err/ERR122/026/ERR12254126/ERR12254126.bam |
| bam_md5 | e5960107cd347e999374bcbee81048d9 |
| base_count | 401654501 |
| binning_software | Not reported |
| bio_material | Not reported |
| bisulfite_protocol | Not reported |
| broad_scale_environmental_context | urban biome |
| broker_name | Not reported |
| cage_protocol | Not reported |
| cell_line | Not reported |
| cell_type | Not reported |
| center_name | University of California San Diego Microbiome Initiative;UCSDMI |
| checklist | ERC000011 |
| chip_ab_provider | Not reported |
| chip_protocol | Not reported |
| chip_target | Not reported |
| collected_by | Not reported |
| collection_date | 2021 |
| collection_date_end | 2021-12-31 |
| collection_date_start | 2021-01-01 |
| completeness_score | Not reported |
| contamination_score | Not reported |
| control_experiment | Not reported |
| country | Germany:Gottingen;Germany |
| cultivar | Not reported |
| culture_collection | Not reported |
| datahub | dcc_metagenome |
| depth | Not reported |
| description | GridION sequencing: qiita_ptid_15275:15088.MRI1952DJAP065.B.16S |
| dev_stage | Not reported |
| disease | Not reported |
| dnase_protocol | Not reported |
| ecotype | Not reported |
| elevation | 150.0 |
| environment_biome | urban biome |
| environment_feature | human-associated habitat |
| environment_material | saliva |
| environmental_medium | saliva |
| environmental_sample | Not reported |
| experiment_accession | ERX11665026 |
| experiment_alias | qiita_ptid_15275:15088.MRI1952DJAP065.B.16S |
| experiment_target | Not reported |
| experiment_title | GridION sequencing: qiita_ptid_15275:15088.MRI1952DJAP065.B.16S |
| 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/ERR122/026/ERR12254126/ERR12254126.fastq.gz |
| fastq_bytes | 346021890 |
| fastq_file_role | GENERATED_FILE |
| fastq_ftp | ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/026/ERR12254126/ERR12254126.fastq.gz |
| fastq_galaxy | ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/026/ERR12254126/ERR12254126.fastq.gz |
| fastq_md5 | 26671502ec55080ffa754b583ca14e32 |
| file_location | Not reported |
| first_created | 2023-11-09 |
| first_public | 2023-11-10 |
| germline | Not reported |
| hi_c_protocol | Not reported |
| host | Homo sapiens |
| host_body_site | UBERON:buccal mucosa |
| 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 | GridION |
| instrument_platform | OXFORD_NANOPORE |
| investigation_type | Not reported |
| isolate | Not reported |
| isolation_source | Not reported |
| last_updated | 2023-11-10 |
| lat | 51.53 |
| library_construction_protocol | 16S_pcr/adapter_ligation |
| library_gen_protocol | Not reported |
| library_layout | SINGLE |
| library_max_fragment_size | Not reported |
| library_min_fragment_size | Not reported |
| library_name | 15088.MRI1952DJAP065.B.16S |
| 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 | human-associated habitat |
| location | 51.53 N 9.93 E |
| location_end | 51.53 N 9.93 E |
| location_start | 51.53 N 9.93 E |
| lon | 9.93 |
| marine_region | Not reported |
| mating_type | Not reported |
| ncbi_reporting_standard | Not reported |
| 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 | 311892 |
| 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 | qiita_ppdid_178493:15088.MRI1952DJAP065.B.16S |
| run_date | Not reported |
| salinity | Not reported |
| sample_accession | SAMEA114596691 |
| sample_alias | qiita_sid_15088:15088.MRI1952DJAP065.B.16S |
| sample_capture_status | Not reported |
| sample_collection | Not reported |
| sample_description | P-MAPS |
| 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 | 15088.MRI1952DJAP065.B.16S |
| sampling_campaign | Not reported |
| sampling_platform | Not reported |
| sampling_site | Not reported |
| scientific_name | human oral metagenome |
| secondary_project | Not reported |
| secondary_sample_accession | ERS16773690 |
| secondary_study_accession | ERP153335 |
| 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 | male |
| 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 | PRJEB68381 |
| study_alias | qiita_sid_15088 |
| study_title | Pancreatitis - Microbiome As Predictor of Severity P-MAPS |
| sub_species | Not reported |
| sub_strain | Not reported |
| submission_accession | ERA27376419 |
| submission_tool | Not reported |
| submitted_aspera | fasp.sra.ebi.ac.uk:/vol1/run/ERR122/ERR12254126/15088.MRI1952DJAP065.B.16S.R1.fastq.gz |
| submitted_bytes | 429350025 |
| submitted_file_role | SUBMISSION_FILE |
| submitted_format | FASTQ |
| submitted_ftp | ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12254126/15088.MRI1952DJAP065.B.16S.R1.fastq.gz |
| submitted_galaxy | ftp.sra.ebi.ac.uk/vol1/run/ERR122/ERR12254126/15088.MRI1952DJAP065.B.16S.R1.fastq.gz |
| submitted_host_sex | Not reported |
| submitted_md5 | 1b92ded78f1f808ae81ee5c97c778c8f |
| submitted_read_type | SINGLE |
| surveillance_target | Not reported |
| tag | env_geo;env_geo:terrestrial |
| 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 | qiita_sid_15088:15088.MRI1952DJAP065.B.16S |
|---|---|
| title | 15088.MRI1952DJAP065.B.16S |
| description | P-MAPS |
| host_height_units | cm |
|---|---|
| year | 2021 |
| host_taxid | 9606 |
| infected_collection | no |
| opioid_name | not collected |
| cardiovascular_disease_in_past | no |
| sequencing | not collected |
| empo_4 | Animal secretion (non-saline) |
| pm_none | yes |
| cholestasis_at_time_of_enrollment | yes |
| empo_2 | Host-associated (non-saline) |
| nsaid | no |
| empo_3 | Animal (non-saline) |
| grade_of_stool | not collected |
| kidney_injury_akin1 | no |
| acute_fluid_collection | no |
| kidney_injury_akin2 | no |
| empo_1 | Host-associated |
| kidney_injury_akin3 | no |
| respiratory_failure_grade_1 | no |
| host_body_habitat | UBERON:oral cavity |
| antibiotic_treatment_before_enrollment | More than 1 month no antibiotics |
| gastrointestinal_cancer_in_past | no |
| heart_failure_in_past | no |
| env_feature | human-associated habitat |
| hepatic_failure | no |
| sirs | 1 |
| host_weight | 82 |
| respiratory_failure_grade_2 | no |
| respiratory_failure_grade_3 | no |
| respiratory_failure_grade_4 | no |
| tag_mg_dl | 50 |
| drainage_required | no |
| inflammatory_bowel_disease | no |
| glc_mg_dl | 252 |
| ercp_with_papillotomy | yes |
| hematologic_failure | no |
| rheumatic_disease_in_past | yes |
| tube_id | P-MAPS_MRI1952DJAP065_B_16S |
| atlanta | 1 |
| clostridioides_diff_infection_in_past | no |
| duodenal_obstruction | no |
| env_package | human-oral |
| length_of_hospital_stay | 3 |
| insulin | no |
| ca_mmol_l | 2,26 |
| collection date | 2021 |
| latitude | 51.53 |
| other_antidiabetics | no |
| host_subject_id | 817 |
| no_food_intake_possible_for_24h | yes |
| env_material | saliva |
| length_of_hospital_stay_binned | short |
| etiology_drugs | not collected |
| time_pain_hosp | <12h |
| diat | omnivour |
| confusion_ad_admission | 2 |
| irb_protocol_id | 02807 |
| pleural_effusion | no |
| env_biome | urban biome |
| mestenterial_thrombosis | no |
| acute_necrotic_collection | no |
| opioid_dose | not collected |
| crea_mg_dl | 0.9 |
| sex | male |
| collection_device | eSwab |
| ct_or_sonographic_drainage | no |
| irritable_stomach_bowel_disease_in_past | no |
| ppi | no |
| metformin | no |
| immunosuppressant | no |
| hematologic_cancer_in_past | yes |
| qiita_sample_type | buccal swab |
| extra_gastrointestinal_cancer_in_past | no |
| statines | no |
| non_invasive_ventilation | no |
| necrosis | no |
| collection_method | buccal |
| geo_loc_name | Germany:Gottingen |
| irb_institute | University medical center Goettingen |
| parkinson_in_past | no |
| specific_current_antibiotics | not collected |
| country | Germany |
| crp_mg_l | 0.2 |
| true_control | TRUE |
| ercp_with_stent_implantation | yes |
| host scientific name | Homo sapiens |
| laxatives | no |
| haps | 0 |
| sample_type | buccal swab |
| eus_drainage_with_pigtails | no |
| collection_timestamp | 2021 |
| ENA-FIRST-PUBLIC | 2023-11-10 |
| hiv | no |
| ENA-LAST-UPDATE | 2023-11-10 |
| walled_off_necrosis | no |
| neuroleptics | no |
| invasive_ventilation | no |
| longitude | 9.93 |
| perotinitis | no |
| host_body_mass_index | 23.95909423 |
| comment4 | not collected |
| comment3 | not collected |
| comment2 | not collected |
| organism | human oral metagenome |
| physical_specimen_remaining | FALSE |
| comment1 | not collected |
| host_body_site | UBERON:buccal mucosa |
| ercp_yes | yes |
| scientific_name | human oral metagenome |
| bisap | 1 |
| abdominal_pain_vas | 10 |
| chronic_constipation_in_past | no |
| ca_mg_dl | not collected |
| host_height | 185 |
| dementia_in_past | no |
| ethic | Caucasian |
| hepatitis_in_past | no |
| life_stage | adult |
| etiology_other | not collected |
| icu_admission | no |
| other_abdominal_surgery | no |
| confusion_at_admission | no |
| chronic_alcohol_consumption | Chronic alcohol consumption |
| eus_drainage_with_lams | no |
| death | no |
| chronic_diarrhea_in_past | no |
| origin | not collected |
| physical_specimen_location | U Gottingen |
| host_body_product | UBERON:saliva |
| pseudocyst | no |
| antidiabetics | no |
| other_neurological_disease | no |
| alcohol_units | 0.1 |
| hkt | 40.7 |
| liver_cirrhosis_in_past | no |
| number_of_opioid_application | not collected |
| paracetamol | no |
| host_common_name | human |
| nicotine_consumption | No |
| bun_mg_dl | 17 |
| geographic location (country and/or sea) | Germany |
| neurologic_failure | no |
| elevation | 150 |
| severity | mild |
| ENA-CHECKLIST | ERC000011 |
| dna_extracted | TRUE |
| diabetes_mellitus_in_past | no |
| center | MRI |
| host_weight_units | kg |
| bowel_intestinal_surgery_in_past | no |
| no_previous_medication | no |
| autism | no |
| cardiovascular_failure_grade_1 | no |
| host_age_units | years |
| other_organ_failure | no |
| cardiovascular_failure_grade_2 | no |
| etiology | biliary |
| leuk_10_3_ml | 27.88 |
| cardiovascular_failure_grade_3 | no |
| nafld | no |
| cardiovascular_failure_grade_4 | no |
| ldh | 342 |
| no_complication | yes |
| host_age | 69 |
| depression_in_past | no |
| other_gastrointestinal_diseases_in_past | no |
| specific_previous_week_antibiotics | not collected |
| opioid_intake | no |
| eus_drainage | no |
| run | ERR12254126 |
|---|---|
| sample | SAMEA114596691 |
| study | PRJEB68381 |
| title | 15088.MRI1952DJAP065.B.16S |
| alias | qiita_sid_15088:15088.MRI1952DJAP065.B.16S |
| site | buccal swab |
| subject | 817 |
| phenotype | Not reported |
| sex | male |
| smoking | Not reported |
| periodontitis | Not reported |
| time_point | Not reported |
| negative_control | False |
| lab_model | False |
| state | complete |
| reads_input | 10000 |
| species_reported | 25 |
| human_primary | True |
Model-based taxonomy; research use. This report does not provide a diagnosis or a validated health score.