Chondrosia reniformis
Info
| NCBI taxon id: | 68574 NCBI; ENA; GoaT |
|---|---|
| Order: | Chondrillida |
| Family: | Chondrillidae |
| NCBI lineage: | Eukaryota;Metazoa;Porifera;Demospongiae;Verongimorpha;Chondrillida;Chondrillidae;Chondrosia; |
| GoaT genome size (M): | 97 (ancestor) |
| GoaT asm span (M): | 117 (direct) |
| GoaT chr no.: | 16 (ancestor) |
| GoaT haploid no.: | 5 (ancestor) |
| GoaT ploidy: | 12 (ancestor) |
| ToLID prefix: | odChoReni |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| odChoReni1 | GHC0000189 | GEOMAR HELMHOLTZ CENTRE | NOT_APPLICABLE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9362048 | SAMEA9362004 |
| odChoReni1 | GHC0000189 | GEOMAR HELMHOLTZ CENTRE | NOT_APPLICABLE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9362051 | SAMEA9362004 |
| odChoReni1 | GHC0000189 | GEOMAR HELMHOLTZ CENTRE | NOT_APPLICABLE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9362040 | SAMEA9362004 |
| odChoReni1 | GHC0000189 | GEOMAR HELMHOLTZ CENTRE | NOT_APPLICABLE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA9362047 | SAMEA9362004 |
| odChoReni1 | GHC0000189 | GEOMAR HELMHOLTZ CENTRE | NOT_APPLICABLE | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA12929236 | SAMEA9362004 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | odChoReni1 | 31 | 34.91 | 123,564,375 | 32.08 | 1.14 | 94.72 | 0.57 |   histogram.txt |
| hic-arima2 | odChoReniRND | 31 | 18.13 | 30,496,898 | 65.00 | 4.57 | 85.69 | 2.12 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | odChoReni1 | 2022-04-22 | TRACTION-RUN-101 | m64229e_220422_155254 | A01 | 1002 | 10,309,736,611 | 14,308 | SAMEA9362055 | ERR10224860 |
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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 | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | odChoReni1 | 2022-08-09 | 45562_2#3 | 87,833,110 | 13,262,799,610 | SAMEA9362038 | ERR10177765 | qc complete | Chondrosia reniformis (1.00) |
| - | odChoReniRND | - | 45413_1#13 | 2,526,542 | 378,981,300 | - | Chondrosia reniformis (1.00) | ||
| - | odChoReniRND | - | 45413_1#23 | 3,315,912 | 497,386,800 | - | Chondrosia reniformis (1.00) | ||
| - | odChoReniRND | - | 45413_1#14 | 2,292,586 | 343,887,900 | - | |||
| - | odChoReniRND | - | 45413_1#11 | 2,166,666 | 324,999,900 | - | |||
| - | odChoReniRND | - | 45413_1#12 | 1,932,260 | 289,839,000 | - | Chondrosia reniformis (1.00) | ||
| - | odChoReniRND | - | 45413_1#15 | 5,681,498 | 852,224,700 | - | Chondrosia reniformis (1.00) | ||
| RNA PolyA | odChoReni1 | 2022-08-23 | 45657_1#91 | 57,691,168 | 8,711,366,368 | SAMEA12929236 | ERR10177766 | qc complete |
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 | info |
|---|---|
| No matching records found | |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
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 | ||
| No matching records found | ||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| odChoReni1 |    |
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
BTK datasets:
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| No matching records found | ||||||||
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