Cercopis vulnerata
Red and black froghopper
Info
| NCBI taxon id: | 279269 NCBI; ENA; GoaT |
|---|---|
| Order: | Hemiptera |
| Family: | Cercopidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Auchenorrhyncha;Cercopoidea;Cercopidae;Cercopidaeincertaesedis;Cercopis; |
| GoaT genome size (M): | 3,467 (ancestor) |
| GoaT asm span (M): | 974 (ancestor) |
| GoaT chr no.: | 15 (ancestor) |
| GoaT haploid no.: | 7 (ancestor) |
| GoaT ploidy: | 3 (ancestor) |
| ToLID prefix: | ihCerVuln |
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 |
|---|---|---|---|---|---|---|
| ihCerVuln1 | Ox000412 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7520629 | SAMEA7520533 |
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 | ihCerVuln1 | 31 | 14.41 | 1,188,675,595 | 51.59 | 0.87 | 97.93 | 0.72 |   histogram.txt |
| pacbio | ihCerVuln1 | 31 | 44.67 | 2,080,320 | 98.38 | 3.46 | 65.81 | 5.67 |   histogram.txt |
| hic-arima2 | ihCerVuln1 | 31 | 54.27 | 801,776,947 | 25.75 | 0.68 | 98.00 | 0.51 |   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 | ihCerVuln1 | 2020-09-26 | 77509 | m64089_200926_150942 | C01 | 1019 | 710,776,991 | 15,129 | SAMEA7520629 | ||
| PacBio - HiFi | ihCerVuln1 | 2020-12-05 | 78722 | m64089_201205_113521 | C01 | 1002 | 428,362,166 | 14,999 | SAMEA7520629 |
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 | ihCerVuln1 | 2020-10-16 | 35192_8#8 | 121,373,894 | 18,327,457,994 | SAMEA7520629 | qc complete | Cercopis sanguinolenta (1.00) | |
| Chromium genome | ihCerVuln1 | 2020-10-16 | 35192_8#7 | 87,786,938 | 13,255,827,638 | SAMEA7520629 | qc complete | Cercopis sanguinolenta (1.00) | |
| Chromium genome | ihCerVuln1 | 2020-10-16 | 35192_8#5 | 95,481,322 | 14,417,679,622 | SAMEA7520629 | qc complete | Cercopis sanguinolenta (1.00) | |
| Chromium genome | ihCerVuln1 | 2020-10-16 | 35192_8#6 | 86,599,968 | 13,076,595,168 | SAMEA7520629 | qc complete | Cercopis (1.00) | |
| Hi-C - Arima v2 | ihCerVuln1 | 2020-10-12 | 35187_2#1 | 842,001,114 | 127,142,168,214 | SAMEA7520629 | qc complete | Cercopis sanguinolenta (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 |
|---|---|
| 0.978312 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.91124 | 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 |
|---|---|
| ihCerVuln1 |    |
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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