Pterostichus strenuus
Info
| NCBI taxon id: | 484362 NCBI; ENA; GoaT |
|---|---|
| Order: | Coleoptera |
| Family: | Carabidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Coleoptera;Adephaga;Caraboidea;Carabidae;Harpalinae;Pterostichini;Pterostichus;Phonias; |
| GoaT genome size (M): | 639 (ancestor) |
| GoaT asm span (M): | 689 (ancestor) |
| GoaT chr no.: | 39 (direct) |
| GoaT haploid no.: | 15 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | icPteStre |
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 |
|---|---|---|---|---|---|---|
| icPteStre1 | Ox001037 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA8603892 | SAMEA8603254 |
| icPteStre1 | Ox001037 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA8603892 | SAMEA8603254 |
| icPteStre1 | Ox001037 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA8603899 | SAMEA8603254 |
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 | icPteStre1 | 31 | 30.55 | 569,301,995 | 40.53 | 1.75 | 97.41 | 0.10 |   histogram.txt |
| 10x | icPteStre1 | 31 | 39.98 | 602,322,074 | 45.33 | 1.88 | 97.97 | 0.38 |   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 | icPteStre1 | 2021-12-02 | 88580 | m64221e_211202_173925 | A01 | 1019 | 13,801,938,459 | 13,581 | SAMEA8603899 | ||
| PacBio - HiFi | icPteStre1 | 2024-04-26 | TRACTION-RUN-1256 | m84047_240426_104952_s1 | A01 | 1019 | 22,172,218,054 | 14,459 | SAMEA8603899 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | icPteStre1 | 2021-06-28 | 38911_4#27 | 116,046,366 | 17,523,001,266 | SAMEA8603892 | qc complete | Pterostichus strenuus (1.00) | |
| Chromium genome | icPteStre1 | 2021-06-28 | 38911_4#26 | 127,107,372 | 19,193,213,172 | SAMEA8603892 | qc complete | Pterostichus strenuus (1.00) | |
| Chromium genome | icPteStre1 | 2021-06-28 | 38911_4#25 | 119,706,336 | 18,075,656,736 | SAMEA8603892 | qc complete | Pterostichus strenuus (1.00) | |
| Chromium genome | icPteStre1 | 2021-06-28 | 38911_4#28 | 132,280,622 | 19,974,373,922 | SAMEA8603892 | qc complete | Pterostichus strenuus (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 |
|---|---|
| 0.930437 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.904322 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.900615 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.900227 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
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 |
|---|---|
| icPteStre1 |    |
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 MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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