Opsius stactogalus
Info
| NCBI taxon id: | 1223885 |
|---|---|
| Order: | Hemiptera |
| Family: | Cicadellidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Auchenorrhyncha;Membracoidea;Cicadellidae;Deltocephalinae;Opsius; |
| GoaT genome size (M): | 4,658 (ancestor) |
| GoaT asm span (M): | 745 (ancestor) |
| GoaT chr no.: | 21 (ancestor) |
| ToLID prefix: | ihOpsStac |
Specimens
Below is information about specimens collected for this species retrieved from the Golden Record manifest.
public_name | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| ihOpsStac1 | NHMUK014444501 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA9065974 | SAMEA9065882 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| 10x | ihOpsStac1 | 31 | 48.9 | 1,186,117,104 | 39.44 | 0.61 | 96.74 | 0.35 |   |
| pacbio | ihOpsStac1 | 31 | 43.27 | 9,869,658 | 72.62 | 4.29 | 80.52 | 4.33 |   |
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 | ihOpsStac1 | 2021-07-12 | 84264 | m64089e_210712_152721 | D01 | 1015 | 3,381,911,746 | 11,361 | SAMEA9065974 |
Illumina run data
Illumina run stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#29 | 325,730,328 | 49,185,279,528 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
| Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#32 | 358,755,554 | 54,172,088,654 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
| Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#30 | 212,190,028 | 32,040,694,228 | SAMEA9065974 | qc complete | Opsius stactogalus (1.00) | |
| Chromium genome | ihOpsStac1 | 2021-07-27 | 39620_2#31 | 281,002,448 | 42,431,369,648 | SAMEA9065974 | qc complete | Opsius stactogalus (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 |
|---|---|
| 0.992513 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
| 0.984086 | NZ_CP013212.1 Candidatus Sulcia muelleri strain PUNC, complete genome |
| 0.921588 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
Species composition by small subunit (SSU) presence in the assembly.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
Re-assembly of reads classified under each identified SSU Marker family.
specimen | family | classified reads | original assembly | re-assembly | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | reads | BUSCO | contigs | contig length | additional reads | circos | ||
| No matching records found | |||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ihOpsStac1 |    |
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 MitoHiFi2.
specimen | asm | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|
| No matching records found | |||||||
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