Dolichovespula norwegica
Norwegian wasp
Info
| NCBI taxon id: | 1799775 NCBI; ENA; GoaT |
|---|---|
| Order: | Hymenoptera |
| Family: | Vespidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Vespoidea;Vespidae;Vespinae;Dolichovespula; |
| GoaT genome size (M): | 312 (ancestor) |
| GoaT asm span (M): | 232 (ancestor) |
| GoaT chr no.: | 50 (ancestor) |
| GoaT haploid no.: | 25 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | iyDolNorw |
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 |
|---|---|---|---|---|---|---|
| iyDolNorw1 | Ox000569 | UNIVERSITY OF OXFORD | MALE | ABDOMEN | SAMEA7701592 | SAMEA7701396 |
| iyDolNorw1 | Ox000569 | UNIVERSITY OF OXFORD | MALE | HEAD | SAMEA7701591 | SAMEA7701396 |
| iyDolNorw1 | Ox000569 | UNIVERSITY OF OXFORD | MALE | THORAX | SAMEA7701591 | SAMEA7701396 |
| iyDolNorw2 | NHMUK014438697 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA115599669 | SAMEA115574621 |
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 | iyDolNorw1 | 31 | 51.66 | 1,993,869 | 95.17 | 4.51 | 82.10 | 6.11 |   histogram.txt |
| 10x | iyDolNorw1 | 31 | 75.75 | 254,990,662 | 35.33 | 0.32 | 98.33 | 0.81 |   histogram.txt |
| hic-arima2 | iyDolNorw1 | 31 | -1 | 0.00 | -100.00 | 0.00 | -100.00 |   histogram.txt | |
| pacbio | iyDolNorw2 | 31 | 19.49 | 305,817,516 | 41.62 | 0.44 | 95.50 | 0.08 |   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 | iyDolNorw1 | 2021-05-14 | 82319 | m64016e_210514_220917 | B01 | 1003 | 1,456,846,285 | 14,095 | SAMEA7701592 | ||
| PacBio - HiFi | iyDolNorw2 | 2025-02-10 | TRACTION-RUN-1765 | m84098_250210_122935_s3 | C01 | 2059 | 12,282,507,547 | 9,414 | SAMEA115599669 |
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 | iyDolNorw1 | 2021-05-26 | 38128_3#35 | 152,884,858 | 23,085,613,558 | SAMEA7701592 | qc complete | Dolichovespula norwegica (1.00) | |
| Chromium genome | iyDolNorw1 | 2021-05-26 | 38128_3#33 | 110,644,140 | 16,707,265,140 | SAMEA7701592 | qc complete | Dolichovespula norwegica (1.00) | |
| Chromium genome | iyDolNorw1 | 2021-05-26 | 38128_3#36 | 76,387,086 | 11,534,449,986 | SAMEA7701592 | qc complete | Dolichovespula norwegica (1.00) | |
| Chromium genome | iyDolNorw1 | 2021-05-26 | 38128_3#34 | 111,119,156 | 16,778,992,556 | SAMEA7701592 | qc complete | Dolichovespula norwegica (1.00) | |
| Hi-C - Arima v2 | iyDolNorw1 | 2021-05-16 | 37941_1#5 | 708,037,378 | 106,913,644,078 | SAMEA7701591 | qc complete | Dolichovespula norwegica (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 |
|---|---|
| 0.97991 | [35 seqs] NZ_BAKW01000035.1 Asaia platycodi JCM 25414 DNA, contig: JCM25414.contig00035, whole genome shotgun sequence [...] |
| 0.957533 | [141 seqs] NZ_AKBR01000001.1 Pseudomonas fluorescens NZ007 scf_11267_4_contig_1, whole genome shotgun sequence [...] |
| 0.952766 | NZ_CP018101.1 Delftia sp. HK171, complete genome |
| 0.905724 | [37 seqs] NZ_LMKI01000001.1 Pseudomonas sp. Leaf15 contig_1, whole genome shotgun sequence [...] |
| 0.904322 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, 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 |
|---|---|
| iyDolNorw1 |    |
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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