Ennomos quercinarius
August thorn
Info
| NCBI taxon id: | 875883 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): | 491 (direct) |
| GoaT chr no.: | 62 (ancestor) |
| GoaT haploid no.: | 29 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilEnnQuei |
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 |
|---|---|---|---|---|---|---|
| ilEnnQuei1 | Ox000699 | UNIVERSITY OF OXFORD | NOT_COLLECTED | ABDOMEN | SAMEA7701756 | SAMEA7701560 |
| ilEnnQuei1 | Ox000699 | UNIVERSITY OF OXFORD | NOT_COLLECTED | THORAX | SAMEA7701755 | SAMEA7701560 |
| ilEnnQuei1 | Ox000699 | UNIVERSITY OF OXFORD | NOT_COLLECTED | HEAD | SAMEA7701755 | SAMEA7701560 |
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 | ilEnnQuei1 | 31 | 52.44 | 540,503,370 | 39.43 | 0.19 | 95.88 | 0.38 |   histogram.txt |
| pacbio | ilEnnQuei1 | 31 | 23.47 | 489,289,051 | 32.31 | 0.24 | 97.95 | 0.16 |   histogram.txt |
| hic-arima2 | ilEnnQuei1 | 31 | 100.2 | 475,072,503 | 29.29 | 0.40 | 97.65 | 0.30 |   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 | ilEnnQuei1 | 2021-03-14 | 80512 | m64097e_210314_154925 | D01 | 1002 | 24,197,042,567 | 14,649 | SAMEA7701756 | ERR6412368 |
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 | ilEnnQuei1 | 2021-03-25 | 37020_4#26 | 169,220,756 | 25,552,334,156 | SAMEA7701756 | ERR6054763 | qc complete | Ennomos quercinaria (1.00) |
| Chromium genome | ilEnnQuei1 | 2021-03-25 | 37020_4#27 | 137,048,982 | 20,694,396,282 | SAMEA7701756 | ERR6054764 | qc complete | Ennomos quercinaria (1.00) |
| Chromium genome | ilEnnQuei1 | 2021-03-25 | 37020_4#28 | 120,317,856 | 18,167,996,256 | SAMEA7701756 | ERR6054765 | qc complete | Ennomos quercinaria (1.00) |
| Chromium genome | ilEnnQuei1 | 2021-03-25 | 37020_4#25 | 154,880,618 | 23,386,973,318 | SAMEA7701756 | ERR6054762 | qc complete | Ennomos quercinaria (0.99) |
| Hi-C - Arima v2 | ilEnnQuei1 | 2021-03-24 | 36948_4#2 | 863,031,906 | 130,317,817,806 | SAMEA7701755 | ERR6054761 | qc complete | Ennomos quercinaria (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 |
|---|---|
| 0.914198 | 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 |
|---|---|
| ilEnnQuei1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ilEnnQuei1 | hicanu | 2021-03-17 | 1,096,541 | 3,736 | 1,046,910,532 | C:99.0%[S:76.2%,D:22.8%],F:0.4%,M:0.6%,n:1367 | - | ||
| ilEnnQuei1 | hicanu.purging | 2021-03-17 | 4,267,015 | 359 | 498,116,648 | C:98.9%[S:98.2%,D:0.7%],F:0.4%,M:0.7%,n:1367 | - | ||
| ilEnnQuei1 | hifiasm.purging_e | 2021-03-17 | 15,954,497 | 67 | 16,835,883 | 49 | 492,069,817 | - | |
| ilEnnQuei1 | hifiasm.scaff_new.salsa | 2021-03-17 | 16,143,522 | 54 | 17,413,370 | 45 | 497,916,682 | - | |
| ilEnnQuei1 | hifiasm.purging | 2021-03-17 | 16,862,296 | 49 | 497,914,911 | C:99.0%[S:98.3%,D:0.7%],F:0.3%,M:0.7%,n:1367 | - | ||
| ilEnnQuei1 | hifiasm.scaff.salsa | 2021-03-17 | 16,143,525 | 54 | 17,413,369 | 45 | 497,916,710 | - | |
| ilEnnQuei1 | hifiasm | 2021-03-17 | 16,475,182 | 143 | 509,856,133 | C:99.0%[S:98.0%,D:1.0%],F:0.3%,M:0.7%,n:1367 | - | ||
| ilEnnQuei1 | hifiasm.purging_40 | 2021-03-17 | 16,862,296 | 45 | 495,127,539 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilEnnQuei1 | mitohifi.reads | mito | 2021-03-17 | 15,680 | 36 | None | True | NC_062170.1; 15,513 bp; 37 genes |
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