Ennomos fuscantarius
Dusky thorn
Info
| NCBI taxon id: | 722662 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Geometridae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Ennomos; |
| GoaT genome size (M): | 831 (ancestor) |
| GoaT asm span (M): | 444 (direct) |
| GoaT chr no.: | 62 (ancestor) |
| GoaT haploid no.: | 29 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilEnnFusc |
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 |
|---|---|---|---|---|---|---|
| ilEnnFusc1 | Ox000201 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7520268 | SAMEA7520184 |
| ilEnnFusc1 | Ox000201 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7520267 | SAMEA7520184 |
| ilEnnFusc1 | Ox000201 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7520267 | SAMEA7520184 |
| ilEnnFusc2 | Ox000200 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7520270 | SAMEA7520185 |
| ilEnnFusc2 | Ox000200 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7520269 | SAMEA7520185 |
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 | ilEnnFusc2 | 31 | 37.69 | 470,366,042 | 33.51 | 0.11 | 96.91 | 0.43 |   histogram.txt |
| pacbio | ilEnnFusc2 | 31 | 26.03 | 440,552,385 | 28.30 | 0.13 | 98.20 | 0.18 |   histogram.txt |
| hic-arima2 | ilEnnFusc2 | 31 | 60.28 | 358,584,602 | 37.41 | 1.27 | 97.98 | 0.45 |   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 | ilEnnFusc2 | 2020-02-02 | TRACTION-RUN-10 | m64097_200202_131657 | C01 | 1001 | 24,285,804,447 | 14,335 | SAMEA7520269 | ERR6560797 |
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 | ilEnnFusc2 | 2020-01-27 | 32841_6#5 | 75,956,732 | 11,469,466,532 | SAMEA7520269 | ERR6054405 | qc complete | Ennomos fuscantaria (1.00) |
| Chromium genome | ilEnnFusc2 | 2020-01-27 | 32841_6#6 | 97,960,284 | 14,792,002,884 | SAMEA7520269 | ERR6054406 | qc complete | Ennomos fuscantaria (1.00) |
| Chromium genome | ilEnnFusc2 | 2020-01-27 | 32841_6#8 | 115,212,680 | 17,397,114,680 | SAMEA7520269 | ERR6054408 | qc complete | Ennomos fuscantaria (1.00) |
| Chromium genome | ilEnnFusc2 | 2020-01-27 | 32841_6#7 | 79,874,836 | 12,061,100,236 | SAMEA7520269 | ERR6054407 | qc complete | Ennomos fuscantaria (1.00) |
| Hi-C - Arima v2 | ilEnnFusc2 | 2020-09-07 | 34997_5#2 | 410,448,076 | 61,977,659,476 | SAMEA7520270 | ERR6054409 | qc complete | Ennomos fuscantaria (1.00) |
| RNA PolyA | ilEnnFusc1 | 2021-03-19 | 36703_6#16 | 49,893,480 | 7,533,915,480 | SAMEA7520267 | ERR6054410 | qc complete | Ennomos fuscantaria (1.00) |
| RNA PolyA | ilEnnFusc1 | 2021-09-17 | 40838_6#5 | 35,413,026 | 5,347,366,926 | SAMEA7520268 | ERR6787420 | qc complete | Ennomos fuscantaria (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 |
|---|---|
| 0.920851 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.900227 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, 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 |
|---|---|
| ilEnnFusc2 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| canu | ccs.purge | 2020-02-10 | 12,866,393 | 108 | 12,895,026 | 90 | 443,503,631 | C:98.2%[S:97.5%,D:0.7%],F:0.5%,M:1.3%,n:1658 | - |
| ilEnnFusc2 | hicanu.purging | 2020-10-15 | 14,135,714 | 116 | 443,454,946 | C:98.4%[S:97.7%,D:0.7%],F:0.5%,M:1.1%,n:1658 | - | ||
| ilEnnFusc2 | hicanu | 2020-10-15 | 3,443,446 | 7,313 | 824,646,644 | C:98.2%[S:36.2%,D:62.0%],F:0.4%,M:1.4%,n:1658 | - | ||
| ilEnnFusc2 | hifiasm | 2020-10-15 | 15,530,463 | 106 | 449,353,268 | C:98.6%[S:97.8%,D:0.8%],F:0.2%,M:1.2%,n:1658 | - | ||
| ilEnnFusc2 | hifiasm.purging | 2020-10-15 | 15,530,463 | 45 | 444,943,190 | C:98.7%[S:98.1%,D:0.6%],F:0.2%,M:1.1%,n:1658 | - | ||
| ilEnnFusc2 | hifiasm.scaffolding.salsa | 2020-10-15 | 15,530,408 | 45 | 15,632,053 | 44 | 444,942,699 | - | |
| ilEnnFusc2 | hifiasm.scaffolding | 2020-10-15 | 15,530,408 | 45 | 15,632,053 | 44 | 444,942,699 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilEnnFusc2 | mitohifi.reads | mito | 2020-10-15 | 15,489 | 36 | None | True | NC_062170.1; 15,513 bp; 37 genes |
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