Ancylus fluviatilis
Info
| NCBI taxon id: | 153587 |
|---|---|
| Order: | Hygrophila |
| Family: | Planorbidae |
| NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Gastropoda;Heterobranchia;Euthyneura;Panpulmonata;Hygrophila;Lymnaeoidea;Ancylidae;Ancylus; |
| GoaT genome size (M): | 1,300 (ancestor) |
| GoaT asm span (M): | 871 (ancestor) |
| GoaT chr no.: | 48 (ancestor) |
| ToLID prefix: | xgAncFluv |
Specimens
Below is information about specimens collected for this species retrieved from the Golden Record manifest.
public_name | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| xgAncFluv1 | NHMUK014361004 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7521066 | SAMEA7520966 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | xgAncFluv1 | 31 | 35.07 | 182,931,108 | 93.53 | 3.28 | 83.87 | 2.62 |   |
| pacbio | xgAncFluv1 | 31 | 37.93 | 452,936 | 74.52 | 2.91 | 76.17 | 6.56 |   |
| hic-arima2 | xgAncFluv1 | 31 | 37.97 | 1,084,474,527 | 50.26 | 11.27 | 92.14 | 0.73 |   |
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 | xgAncFluv1 | 2020-09-11 | 77367 | m64125_200911_153315 | B01 | 1002 | 283,336,930 | 10,154 | SAMEA7521066 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | xgAncFluv1 | 2020-11-16 | 35281_7#3 | 64,374,404 | 9,720,535,004 | SAMEA7521066 | qc complete | Ancylus fluviatilis (1.00) | |
| Chromium genome | xgAncFluv1 | 2020-11-16 | 35281_7#1 | 94,566,206 | 14,279,497,106 | SAMEA7521066 | qc complete | Ancylus fluviatilis (1.00) | |
| Chromium genome | xgAncFluv1 | 2020-11-16 | 35281_7#2 | 56,801,592 | 8,577,040,392 | SAMEA7521066 | qc complete | Ancylus fluviatilis (1.00) | |
| Chromium genome | xgAncFluv1 | 2020-11-16 | 35281_7#4 | 51,458,760 | 7,770,272,760 | SAMEA7521066 | qc complete | ||
| Hi-C - Arima v2 | xgAncFluv1 | 2020-10-20 | 35219_5#1 | 853,899,856 | 128,938,878,256 | SAMEA7521066 | 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.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
Re-assembly of reads classified under each identified SSU Marker family.
specimen | family | classified reads | original assembly | re-assembly | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | reads | BUSCO | contigs | contig length | additional reads | circos | ||
| No matching records found | |||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| xgAncFluv1 |    |
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 | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi2.
specimen | asm | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|
| No matching records found | |||||||
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