Backend is in debug mode
This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000005Q.1

At a glance

Bacterial overview
[{"label":"16S species","name":"sixteenSSpecies","customDisplay":{"type":"htmlTemplate","html":"<bacterial-overview>__value__</bacterial-overview>","displayGroup":"bacterialOverview","label":"Bacterial overview"},"value":"Klebsiella pneumoniae strain DSM 30104 16S ribosomal RNA, partial sequence","header":"At a glance","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":10},{"label":"MLST sequence type","name":"mlstSequenceType","customDisplay":{"type":"htmlTemplate","html":"<bacterial-overview>__value__</bacterial-overview>","displayGroup":"bacterialOverview","label":"Bacterial overview"},"value":"9279","header":"At a glance","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":20},{"label":"AMRFinderPlus hit count","name":"amrfinderplusHitCount","customDisplay":{"type":"htmlTemplate","html":"<bacterial-overview>__value__</bacterial-overview>","displayGroup":"bacterialOverview","label":"Bacterial overview"},"value":42,"header":"At a glance","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":30},{"label":"Contig count","name":"contigCount","customDisplay":{"type":"htmlTemplate","html":"<bacterial-overview>__value__</bacterial-overview>","displayGroup":"bacterialOverview","label":"Bacterial overview"},"value":71,"header":"At a glance","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":40},{"label":"N50","name":"n50","customDisplay":{"type":"htmlTemplate","html":"<bacterial-overview>__value__</bacterial-overview>","displayGroup":"bacterialOverview","label":"Bacterial overview"},"value":314578,"header":"At a glance","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":50}]

Typing

MLST and ribosomal typing
[{"label":"MLST schema","name":"mlstSchema","customDisplay":{"type":"htmlTemplate","html":"<bacterial-typing-details>__value__</bacterial-typing-details>","displayGroup":"bacterialTyping","label":"MLST and ribosomal typing"},"value":"klebsiella","header":"Typing","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":210},{"label":"MLST alleles","name":"mlstAlleles","customDisplay":{"type":"htmlTemplate","html":"<bacterial-typing-details>__value__</bacterial-typing-details>","displayGroup":"bacterialTyping","label":"MLST and ribosomal typing"},"value":"gapA(2), infB(1), mdh(379), pgi(1), phoE(9), rpoB(4), tonB(12)","header":"Typing","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":220},{"label":"16S alignment length","name":"sixteenSAlignmentLength","customDisplay":{"type":"htmlTemplate","html":"<bacterial-typing-details>__value__</bacterial-typing-details>","displayGroup":"bacterialTyping","label":"MLST and ribosomal typing"},"value":660,"header":"Typing","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":240},{"label":"16S alignment identity","name":"sixteenSAlignmentIdentity","customDisplay":{"type":"htmlTemplate","html":"<bacterial-typing-details>__value__</bacterial-typing-details>","displayGroup":"bacterialTyping","label":"MLST and ribosomal typing"},"value":100,"header":"Typing","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":250}]

AMR

AMRFinderPlus profile
[{"label":"AMRFinderPlus genes","name":"amrfinderplusGenes","customDisplay":{"type":"htmlTemplate","html":"<bacterial-amr-profile>__value__</bacterial-amr-profile>","displayGroup":"bacterialAmr","label":"AMRFinderPlus profile"},"value":"mchF;blaSHV-11;oqxA;oqxB19;kdeA;emrD;fieF;iucA;iucB;iucC;iutA;terE;terD;terC;terB;terA;fosA;ybtQ;ybtP;clbN;silS;silR;silC;silF;silB;silA;silP;pcoA;pcoB;pcoC;pcoD;pcoR;pcoS;clbB;rmpA;rmpD;rmpC;peg-344;iroN;iroD;iroC;iroB","header":"AMR","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":310},{"label":"AMRFinderPlus classes","name":"amrfinderplusClasses","customDisplay":{"type":"htmlTemplate","html":"<bacterial-amr-profile>__value__</bacterial-amr-profile>","displayGroup":"bacterialAmr","label":"AMRFinderPlus profile"},"value":"BETA-LACTAM;NITROFURAN/PHENICOL/QUINOLONE/TETRACYCLINE;PHENICOL/QUINOLONE;EFFLUX;TELLURIUM;FOSFOMYCIN;COPPER/SILVER;SILVER;COPPER","header":"AMR","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":320},{"label":"AMRFinderPlus element types","name":"amrfinderplusElementTypes","customDisplay":{"type":"htmlTemplate","html":"<bacterial-amr-profile>__value__</bacterial-amr-profile>","displayGroup":"bacterialAmr","label":"AMRFinderPlus profile"},"value":"VIRULENCE;AMR;STRESS","header":"AMR","type":{"kind":"metadata","metadataType":"string"},"orderOnDetailsPage":330}]

Assembly QC

Assembly QC
[{"label":"Total length","name":"totalLength","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":5667128,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":410},{"label":"Largest contig","name":"largestContig","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":1110087,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":420},{"label":"N75","name":"n75","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":187259,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":430},{"label":"L50","name":"l50","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":5,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":440},{"label":"L75","name":"l75","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":11,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"int"},"orderOnDetailsPage":450},{"label":"Ambiguous bases per 100 kbp","name":"ambiguousBasesPer100Kbp","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":0,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":460},{"label":"GC percent","name":"gcPercent","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":57.17,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":470},{"label":"CheckM completeness","name":"checkmCompleteness","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":97.93,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":480},{"label":"CheckM contamination","name":"checkmContamination","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":0,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":490},{"label":"CheckM heterogeneity","name":"checkmHeterogeneity","customDisplay":{"type":"htmlTemplate","html":"<bacterial-assembly-qc>__value__</bacterial-assembly-qc>","displayGroup":"bacterialAssemblyQc","label":"Assembly QC"},"value":0,"header":"Assembly QC","type":{"kind":"metadata","metadataType":"float"},"orderOnDetailsPage":500}]

Submission details

Submission ID
SAMN46830210
Version comment
AllTheBacteria Incremental_release_2025-05; ENA run SRR32345642; study PRJNA1219236; ENA collection_date=2021-06-16; sampleCollectionDate uses ENA collection_date for prototype upload
Submitting group
Date submitted
2026-06-20 00:05:26 UTC
Date released
2026-06-20 00:10:11 UTC

Collection Details

Collection date
2021-06-16
Country
China: Beijing

Submission Details

Submitting lab
SUB15064464

IMMense

Workflow notes
IMMense Loculus workflow: QUAST, MLST, 16S, CheckM, and AMRFinderPlus modules

Files

Assembly FASTA
IMMense merged quality TSV
16S BLAST TSV
CheckM output TSV
AMRFinderPlus TSV