Lomaspilis marginata
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Info
| NCBI taxon id: | 722666 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Geometridae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Lomaspilis; |
| GoaT genome size (M): | 831 (ancestor) |
| GoaT asm span (M): | 486 (ancestor) |
| GoaT chr no.: | 62 (ancestor) |
| GoaT haploid no.: | 31 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilLomMarg |
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 |
|---|---|---|---|---|---|---|
| ilLomMarg1 | Ox000630 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7701669 | SAMEA7701492 |
| ilLomMarg1 | Ox000630 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7701669 | SAMEA7701492 |
| ilLomMarg1 | Ox000630 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7701669 | SAMEA7701492 |
| ilLomMarg1 | Ox000630 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7701669 | SAMEA7701492 |
| ilLomMarg1 | Ox000630 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA7701669 | SAMEA7701492 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | ilLomMarg1 | 31 | 34.87 | 3,848,373 | 88.32 | 3.59 | 87.18 | 4.49 |   histogram.txt |
| 10x | ilLomMarg1 | 31 | 30.55 | 629,550,319 | 42.98 | 1.83 | 98.58 | 0.38 |   histogram.txt |
| hic-arima2 | ilLomMarg2 | 31 | 74.63 | 545,069,513 | 66.37 | 5.21 | 95.55 | 0.37 |   histogram.txt |
| pacbio | ilLomMarg3 | 31 | 34.84 | 8,823,939 | 88.14 | 3.80 | 84.66 | 4.21 |   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 | ilLomMarg1 | 2021-04-10 | 81230 | m64221e_210410_143943 | B01 | 1017 | 1,116,990,292 | 14,938 | SAMEA7701669 | ||
| PacBio - HiFi | ilLomMarg3 | 2025-02-11 | TRACTION-RUN-1769 | m84047_250211_114153_s3 | A01 | 2061 | 2,337,771,802 | 12,853 | SAMEA112222261 |
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 | ilLomMarg1 | 2021-04-06 | 37204_4#25 | 91,194,176 | 13,770,320,576 | SAMEA7701669 | qc complete | Lomaspilis marginata (1.00) | |
| Chromium genome | ilLomMarg1 | 2021-04-06 | 37204_4#27 | 76,698,620 | 11,581,491,620 | SAMEA7701669 | qc complete | Lomaspilis marginata (1.00) | |
| Chromium genome | ilLomMarg1 | 2021-04-06 | 37204_4#26 | 104,428,856 | 15,768,757,256 | SAMEA7701669 | qc complete | Lomaspilis marginata (1.00) | |
| Chromium genome | ilLomMarg1 | 2021-04-06 | 37204_4#28 | 120,588,238 | 18,208,823,938 | SAMEA7701669 | qc complete | Lomaspilis marginata (1.00) | |
| Hi-C - Arima v2 | ilLomMarg2 | 2022-03-18 | 44177_1#7 | 754,629,622 | 113,949,072,922 | SAMEA10978862 | qc complete | Lomaspilis marginata (1.00) | |
| RNA PolyA | ilLomMarg2 | 2025-06-09 | 50494_4#37 | 112,807,406 | 17,033,918,306 | SAMEA10978863 | qc complete | Lomaspilis marginata (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 |
|---|---|
| 0.977718 | [426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...] |
| 0.973912 | [3 seqs] NC_014306.1 Erwinia billingiae strain Eb661 complete chromosome [...] |
| 0.912148 | NC_021774.1 Salmonella phage FSL SP-004, complete genome |
| 0.905028 | NZ_CP018101.1 Delftia sp. HK171, complete genome |
| 0.904677 | [120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...] |
| 0.900615 | 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 |
|---|---|
| ilLomMarg1 |    |
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 | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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