Pisidium nitidum
shining pea clam
Info
| NCBI taxon id: | 192231 |
|---|---|
| Order: | Venerida |
| Family: | Sphaeriidae |
| NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Bivalvia;Autobranchia;Heteroconchia;Euheterodonta;Imparidentia;Neoheterodontei;Venerida;Cyrenoidea;Sphaeriidae;Pisidium; |
| GoaT genome size (M): | 1,965 (ancestor) |
| GoaT asm span (M): | unknown (unknown) |
| GoaT chr no.: | 28 (ancestor) |
| ToLID prefix: | xbPisNiti |
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 |
|---|---|---|---|---|---|---|
| xbPisNiti1 | NHMUK014360931 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7520861 | SAMEA7520809 |
| xbPisNiti2 | NHMUK014360799 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7521316 | SAMEA7521216 |
| xbPisNiti3 | NHMUK014361177 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7521404 | SAMEA7521327 |
| xbPisNiti4 | NHMUK014361603 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7521415 | SAMEA7521338 |
| xbPisNiti5 | NHMUK014361619 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7521420 | SAMEA7521342 |
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 | xbPisNiti1 | 31 | 18.27 | 1,651,088,627 | 59.81 | 15.22 | 88.27 | 0.83 |   |
| pacbio | xbPisNiti1 | 31 | 34.51 | 3,890,821 | 80.18 | 3.53 | 88.60 | 5.36 |   |
| hic-arima2 | xbPisNiti2 | 31 | 23.08 | 1,222,112,833 | 63.39 | 8.20 | 91.53 | 1.09 |   |
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 | xbPisNiti1 | 2020-08-28 | 77230 | m64125_200828_155113 | A01 | 1012 | 1,486,460,110 | 11,940 | SAMEA7520861 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | xbPisNiti1 | 2020-10-13 | 35188_7#1 | 188,661,412 | 28,487,873,212 | SAMEA7520861 | qc complete | Pisidium nitidum (1.00) | |
| Chromium genome | xbPisNiti1 | 2020-10-13 | 35188_7#2 | 149,481,960 | 22,571,775,960 | SAMEA7520861 | qc complete | Pisidium nitidum (1.00) | |
| Chromium genome | xbPisNiti1 | 2020-10-13 | 35188_7#3 | 206,384,302 | 31,164,029,602 | SAMEA7520861 | qc complete | ||
| Chromium genome | xbPisNiti1 | 2020-10-13 | 35188_7#4 | 168,295,380 | 25,412,602,380 | SAMEA7520861 | qc complete | Pisidium nitidum (0.99) | |
| Hi-C - Arima v2 | xbPisNiti2 | 2022-12-06 | 46311_3#1 | 654,607,408 | 98,845,718,608 | SAMEA7521316 | qc complete | Pisidium nitidum (1.00) | |
| RNA PolyA | xbPisNiti7 | 2021-05-25 | 37935_5#5 | 41,668,040 | 6,291,874,040 | SAMEA7521433 | qc complete | Pisidium nitidum (1.00) |
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 |
|---|---|
| xbPisNiti1 |    |
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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