Drepanepteryx phalaenoides
Info
| NCBI taxon id: | 560898 NCBI; ENA; GoaT |
|---|---|
| Order: | Neuroptera |
| Family: | Hemerobiidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Neuroptera;Hemerobiiformia;Hemerobiidae;Drepanepteryx; |
| GoaT genome size (M): | 474 (ancestor) |
| GoaT asm span (M): | 467 (ancestor) |
| GoaT chr no.: | 14 (ancestor) |
| GoaT haploid no.: | 7 (ancestor) |
| GoaT ploidy: | 6 (ancestor) |
| ToLID prefix: | inDrePhal |
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 |
|---|---|---|---|---|---|---|
| inDrePhal1 | Ox000225 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7520465 | SAMEA7520373 |
| inDrePhal1 | Ox000225 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7520464 | SAMEA7520373 |
| inDrePhal1 | Ox000225 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7520464 | SAMEA7520373 |
| inDrePhal2 | NHMUK014446981 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | ABDOMEN | SAMEA7696509 | SAMEA7696447 |
| inDrePhal2 | NHMUK014446981 | NATURAL HISTORY MUSEUM | NOT_COLLECTED | THORAX | SAMEA7696508 | SAMEA7696447 |
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 | inDrePhal1 | 31 | 14.36 | 1,009,793,100 | 56.91 | 1.46 | 98.85 | 0.47 |   histogram.txt |
| pacbio | inDrePhal1 | 31 | 37.12 | 51,272,453 | 93.91 | 3.08 | 85.43 | 2.61 |   histogram.txt |
| hic-arima2 | inDrePhal1 | 31 | 35.52 | 1,454,750,569 | 73.38 | 0.55 | 96.91 | 0.37 |   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 | inDrePhal1 | 2020-05-20 | TRACTION-RUN-33 | m64016_200520_142005 | A01 | 1019 | 8,659,983,124 | 13,133 | SAMEA7520464 |
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 | inDrePhal1 | 2020-10-13 | 35188_4#8 | 69,904,538 | 10,555,585,238 | SAMEA7520464 | qc complete | Drepanepteryx phalaenoides (1.00) | |
| Chromium genome | inDrePhal1 | 2020-10-13 | 35188_4#6 | 85,350,472 | 12,887,921,272 | SAMEA7520464 | qc complete | Drepanepteryx phalaenoides (1.00) | |
| Chromium genome | inDrePhal1 | 2020-10-13 | 35188_4#7 | 66,889,402 | 10,100,299,702 | SAMEA7520464 | qc complete | Drepanepteryx phalaenoides (1.00) | |
| Chromium genome | inDrePhal1 | 2020-10-13 | 35188_4#5 | 84,820,046 | 12,807,826,946 | SAMEA7520464 | qc complete | Drepanepteryx phalaenoides (1.00) | |
| Hi-C - Arima v2 | inDrePhal1 | 2020-11-16 | 35436_3#1 | 959,733,732 | 144,919,793,532 | SAMEA7520464 | qc complete | Drepanepteryx phalaenoides (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 |
|---|---|
| 0.961868 | NZ_CP006568.1 Candidatus Sodalis pierantonius str. SOPE, complete genome |
| 0.928588 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.909686 | [2 seqs] NZ_CP006569.1 Sodalis praecaptivus strain HS1, complete genome [...] |
| 0.903242 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, 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 |
|---|---|
| inDrePhal1 |    |
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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