Coreus marginatus
Dock bug
Info
| NCBI taxon id: | 1545300 NCBI; ENA; GoaT |
|---|---|
| Order: | Hemiptera |
| Family: | Coreidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Heteroptera;Panheteroptera;Pentatomomorpha;Coreoidea;Coreidae;Coreinae;Coreus; |
| GoaT genome size (M): | 3,237 (ancestor) |
| GoaT asm span (M): | 1,106 (ancestor) |
| GoaT chr no.: | 22 (direct) |
| GoaT haploid no.: | 11 (direct) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ihCorMarg |
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 |
|---|---|---|---|---|---|---|
| ihCorMarg1 | Ox000228 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7520426 | SAMEA7520343 |
| ihCorMarg1 | Ox000228 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7520426 | SAMEA7520343 |
| ihCorMarg1 | Ox000228 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7520425 | SAMEA7520343 |
| ihCorMarg2 | NHMUK010635099 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA7849298 | SAMEA7849236 |
| ihCorMarg2 | NHMUK010635099 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | HEAD | SAMEA7849298 | SAMEA7849236 |
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 | ihCorMarg1 | 31 | 16.82 | 708,127,740 | 78.17 | 8.91 | 77.96 | 1.61 |   histogram.txt |
| pacbio | ihCorMarg1 | 31 | 40.57 | 18,155,570 | 40.88 | 0.62 | 95.23 | 2.78 |   histogram.txt |
| hic-arima2 | ihCorMarg1 | 31 | 23.53 | 2,040,441,640 | 70.13 | 4.02 | 98.13 | 0.46 |   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 | ihCorMarg1 | 2020-02-29 | TRACTION-RUN-19 | m64094_200229_151649 | B01 | 1021 | 555,409,241 | 12,373 | SAMEA7520425 | ||
| PacBio - HiFi | ihCorMarg1 | 2020-07-27 | TRACTION-RUN-42 | m64016_200727_155308 | D01 | 1016 | 543,757,431 | 12,495 | SAMEA7520425 | ||
| PacBio - HiFi | ihCorMarg1 | 2020-10-31 | 78010 | m64089_201031_112458 | C01 | 1009 | 2,439,061,308 | 10,139 | SAMEA7520425 |
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 | ihCorMarg1 | 2020-08-27 | 34893_6#5 | 82,389,600 | 12,440,829,600 | SAMEA7520425 | qc complete | Coreus marginatus (1.00) | |
| Chromium genome | ihCorMarg1 | 2020-08-27 | 34893_6#8 | 94,476,124 | 14,265,894,724 | SAMEA7520425 | qc complete | Coreus marginatus (1.00) | |
| Chromium genome | ihCorMarg1 | 2020-08-27 | 34893_6#6 | 84,455,454 | 12,752,773,554 | SAMEA7520425 | qc complete | Coreus marginatus (1.00) | |
| Chromium genome | ihCorMarg1 | 2020-08-27 | 34893_6#7 | 98,243,654 | 14,834,791,754 | SAMEA7520425 | qc complete | Coreus marginatus (1.00) | |
| Hi-C - Arima v2 | ihCorMarg1 | 2020-10-07 | 35152_4#1 | 914,403,970 | 138,074,999,470 | SAMEA7520426 | qc complete | Coreus marginatus (1.00) | |
| RNA PolyA | ihCorMarg3 | 2023-08-03 | 47585_1#8 | 82,099,292 | 12,396,993,092 | SAMEA9065899 | qc complete | Coreus marginatus (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 |
|---|---|
| 0.964978 | [426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...] |
| 0.927742 | [26 seqs] NZ_LMPF01000001.1 Burkholderia sp. Leaf177 contig_1, whole genome shotgun sequence [...] |
| 0.918565 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.907417 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
| 0.901759 | [94 seqs] NZ_LWMI01000001.1 Candidatus Arsenophonus triatominarum strain ATi contig000001, whole genome shotgun sequence [...] |
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 |
|---|---|
| ihCorMarg1 |    |
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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