Bathymodiolus septemdierum
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Info
| NCBI taxon id: | 220392 NCBI; ENA; GoaT |
|---|---|
| Order: | Mytiloida |
| Family: | Mytilidae |
| NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Bivalvia;Autobranchia;Pteriomorphia;Mytilida;Mytiloidea;Mytilidae;Bathymodiolinae;Bathymodiolus; |
| GoaT genome size (M): | 1,452 (ancestor) |
| GoaT asm span (M): | 1,428 (direct) |
| GoaT chr no.: | 38 (ancestor) |
| GoaT haploid no.: | 14 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | xbBatSept |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
| tolid | specimen_id | gal | collector_affiliation | date_of_collection | sex | organism_part | biosample | biospecimen | lifestage | symbiont | family | order or group | genus | taxon_id | scientific_name | common_name | tube_or_well_id |
|---|
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
| source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
| pipeline | model | specimen | sample | date | instrument | run id | movie | well | movie length | tag | tag sequence | library load name | reads | yield | N50 | PCR dups (%) | filtered (%) | A (%) | C (%) | G (%) | T (%) | sample accession | run accession | exp accession | study accession | species | barcode |
|---|
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
| pipeline | model | specimen | sample | date | instrument | run id | flowcell | type | library name | reads | yield | N50 | A (%) | C (%) | G (%) | T (%) | sample accession | species | report |
|---|
Illumina run data
Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.
| pipeline | model | source | specimen | date | run id | read pairs | yield | avg qual | avg length | mapped bases (%) | dups (%) | MQ0 (%) | avg insert | sample accession | run accession | exp accession | study accession | sample | tag sequence | tag2 sequence | run status | npg status | species | barcode |
|---|
Cobionts
Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.
| identity | shared-hashes | median-multiplicity | p-value | query | info |
|---|
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
| specimen | contig | SSU length | attributed taxonomy by SSU | cluster |
|---|
MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.
| specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
| specimen | visualisation |
|---|
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
- Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
- FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
- Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
- Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
- Connections_Base: Number of Hi-C connections per base pair
Assemblies
In-progress assembly QC.
| specimen | asm | asm version | date | contig N50 | contigs | largest contig | scaffold N50 | scaffolds | largest scaffold | length | BUSCO | BUSCO lineage | BUSCO version | merqury | pretext |
|---|
Organelles
In-progress organelle results from MitoHiFi or Oatk.
| specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | shared | unique | missing | reference |
|---|
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