Clytus arietis
Wasp beetle
Info
| NCBI taxon id: | 132597 NCBI; ENA; GoaT |
|---|---|
| Order: | Coleoptera |
| Family: | Cerambycidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Coleoptera;Polyphaga;Cucujiformia;Chrysomeloidea;Cerambycidae;Cerambycinae;Clytini;Clytus; |
| GoaT genome size (M): | 528 (ancestor) |
| GoaT asm span (M): | 687 (ancestor) |
| GoaT chr no.: | 20 (direct) |
| GoaT haploid no.: | 10 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | icClyArie |
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 |
|---|---|---|---|---|---|---|
| icClyArie1 | Ox000566 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7701431 | SAMEA7701330 |
| icClyArie1 | Ox000566 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7701431 | SAMEA7701330 |
| icClyArie1 | Ox000566 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7701432 | SAMEA7701330 |
| icClyArie2 | NHMUK014036932 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | ABDOMEN | SAMEA112221892 | SAMEA112221810 |
| icClyArie2 | NHMUK014036932 | NATURAL HISTORY MUSEUM | NOT_PROVIDED | HEAD | SAMEA112222118 | SAMEA112221810 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10x | icClyArie1 | 31 | 19.48 | 1,096,070,234 | 53.94 | 2.06 | 98.63 | 0.37 |   histogram.txt |
| pacbio | icClyArie1 | 31 | 11.21 | 1,067,009,331 | 50.20 | 1.86 | 98.38 | 0.16 |   histogram.txt |
| hic-arima2 | icClyArie1 | 31 | 36.63 | 1,075,156,946 | 0.00 | 100.00 | 2.94 | 0.19 |   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 | icClyArie1 | 2021-03-13 | 80510 | m64125e_210313_151020 | C01 | 1012 | 12,307,081,932 | 11,856 | SAMEA7701432 | ||
| PacBio - HiFi | icClyArie1 | 2021-03-20 | 80717 | m64178e_210320_161720 | B01 | 1012 | 12,921,478,234 | 11,009 | SAMEA7701432 |
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 | icClyArie1 | 2021-03-23 | 36958_4#44 | 135,108,036 | 20,401,313,436 | SAMEA7701432 | qc complete | Clytus arietis (1.00) | |
| Chromium genome | icClyArie1 | 2021-03-23 | 36958_4#41 | 107,713,340 | 16,264,714,340 | SAMEA7701432 | qc complete | Clytus arietis (1.00) | |
| Chromium genome | icClyArie1 | 2021-03-23 | 36958_4#43 | 103,545,748 | 15,635,407,948 | SAMEA7701432 | qc complete | Clytus arietis (1.00) | |
| Chromium genome | icClyArie1 | 2021-03-23 | 36958_4#42 | 91,244,878 | 13,777,976,578 | SAMEA7701432 | qc complete | Clytus arietis (1.00) | |
| Hi-C - Arima v2 | icClyArie1 | 2021-04-07 | 37178_4#6 | 687,241,930 | 103,773,531,430 | SAMEA7701431 | qc complete | Clytus arietis (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 |
|---|---|
| 0.956847 | [157 seqs] NZ_LSYX01000001.1 Wolbachia endosymbiont of Dactylopius coccus strain wDacA Contig_1, whole genome shotgun sequence [...] |
| 0.929005 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.921098 | [256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...] |
| 0.906409 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.906067 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.903242 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.902135 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.900227 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
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 |
|---|---|
| icClyArie1 |    |
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 | reference |
|---|---|---|---|---|---|---|---|---|
| No matching records found | ||||||||
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