Vespula germanica
German wasp
Info
| NCBI taxon id: | 30212 NCBI; ENA; GoaT |
|---|---|
| Order: | Hymenoptera |
| Family: | Vespidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Vespoidea;Vespidae;Vespinae;Vespula; |
| GoaT genome size (M): | 224 (direct) |
| GoaT asm span (M): | 205 (direct) |
| GoaT chr no.: | 50 (ancestor) |
| GoaT haploid no.: | 25 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | iyVesGerm |
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 |
|---|---|---|---|---|---|---|
| iyVesGerm1 | Ox000121 | UNIVERSITY OF OXFORD | FEMALE | THORAX | SAMEA7520575 | SAMEA7520501 |
| iyVesGerm1 | Ox000121 | UNIVERSITY OF OXFORD | FEMALE | HEAD | SAMEA7520575 | SAMEA7520501 |
| iyVesGerm1 | Ox000121 | UNIVERSITY OF OXFORD | FEMALE | ABDOMEN | SAMEA7520576 | SAMEA7520501 |
| iyVesGerm2 | NHMUK010635102 | NATURAL HISTORY MUSEUM | FEMALE | HEAD | SAMEA7849305 | SAMEA7849239 |
| iyVesGerm2 | NHMUK010635102 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA7849306 | SAMEA7849239 |
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 | iyVesGerm1 | 31 | 90.57 | 210,215,552 | 19.52 | 0.24 | 99.12 | 0.53 |   histogram.txt |
| pacbio | iyVesGerm1 | 31 | 35.86 | 198,639,042 | 14.49 | 0.25 | 96.46 | 0.13 |   histogram.txt |
| hic-arima2 | iyVesGerm1 | 31 | 53.37 | 168,429,294 | 10.27 | 0.64 | 98.72 | 0.67 |   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 | iyVesGerm1 | 2020-02-17 | TRACTION-RUN-13 | m64094_200217_145414 | D01 | 1011 | 14,850,466,427 | 12,132 | SAMEA7520575 | ERR6635596 |
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 | iyVesGerm1 | 2020-03-04 | 33431_8#3 | 83,627,532 | 12,627,757,332 | SAMEA7520575 | ERR6054560 | qc complete | Vespula germanica (1.00) |
| Chromium genome | iyVesGerm1 | 2020-03-04 | 33431_8#1 | 107,803,848 | 16,278,381,048 | SAMEA7520575 | ERR6054558 | qc complete | Vespula germanica (1.00) |
| Chromium genome | iyVesGerm1 | 2020-03-04 | 33431_8#4 | 96,665,174 | 14,596,441,274 | SAMEA7520575 | ERR6054561 | qc complete | Vespula germanica (1.00) |
| Chromium genome | iyVesGerm1 | 2020-03-04 | 33431_8#2 | 122,278,402 | 18,464,038,702 | SAMEA7520575 | ERR6054559 | qc complete | Vespula germanica (1.00) |
| Hi-C - Arima v2 | iyVesGerm1 | 2020-09-08 | 34957_4#2 | 61,564,048 | 9,296,171,248 | SAMEA7520575 | ERR6054563 | qc complete | Vespula germanica (1.00) |
| Hi-C - Arima v2 | iyVesGerm1 | 2020-09-08 | 34957_3#2 | 61,836,428 | 9,337,300,628 | SAMEA7520575 | ERR6054562 | qc complete | Vespula germanica (1.00) |
| Hi-C - Arima v2 | iyVesGerm1 | 2020-09-08 | 34957_5#2 | 61,268,122 | 9,251,486,422 | SAMEA7520575 | ERR6054564 | qc complete | Vespula germanica (1.00) |
| RNA PolyA | iyVesGerm2 | 2024-03-15 | 48593_1#11 | 61,971,562 | 9,357,705,862 | SAMEA7849304 | qc complete | Vespula germanica (1.00) | |
| RNA PolyA | iyVesGerm1 | 2021-05-25 | 37935_8#1 | 33,308,904 | 5,029,644,504 | SAMEA7520575 | ERR6286717 | qc complete | Vespula germanica (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 |
|---|---|
| 0.91616 | 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 |
|---|---|
| iyVesGerm1 |    |
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
BTK datasets:
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| iyVesGerm1 | hicanu.purging | 2020-10-15 | 5,039,226 | 188 | 213,505,292 | C:99.4%[S:98.6%,D:0.8%],F:0.2%,M:0.4%,n:1658 | - | ||
| iyVesGerm1 | hicanu.scaff.salsa | 2020-10-15 | 4,555,917 | 193 | 6,086,261 | 162 | 213,521,711 | - | |
| iyVesGerm1 | hicanu.scaff | 2020-10-15 | 5,039,291 | 188 | 6,444,135 | 153 | 213,523,711 | - | |
| iyVesGerm1 | hicanu | 2020-10-15 | 1,016,410 | 1,806 | 423,550,057 | C:99.3%[S:10.0%,D:89.3%],F:0.4%,M:0.3%,n:1658 | - | ||
| iyVesGerm1 | hifiasm.scaff_.salsa | 2020-10-15 | 6,563,385 | 82 | 8,646,363 | 72 | 207,503,886 | - | |
| iyVesGerm1 | hifiasm.scaff_ | 2020-10-15 | 6,563,385 | 78 | 8,944,330 | 68 | 207,503,886 | - | |
| iyVesGerm1 | hifiasm | 2020-10-15 | 6,563,413 | 150 | 212,038,465 | C:99.5%[S:99.1%,D:0.4%],F:0.2%,M:0.3%,n:1658 | - | ||
| iyVesGerm1 | hifiasm.purging | 2020-10-15 | 6,563,413 | 78 | 207,499,979 | C:99.4%[S:99.2%,D:0.2%],F:0.2%,M:0.4%,n:1658 | - | ||
| iyVesGerm1 | hifiasm.scaff.salsa | 2020-10-15 | 6,563,324 | 82 | 8,646,358 | 72 | 207,503,651 | - | |
| iyVesGerm1 | hifiasm.scaff | 2020-10-15 | 6,563,324 | 78 | 8,944,314 | 68 | 207,503,651 | - |
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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