Agonopterix arenella
Brindled Flat-body
Info
| NCBI taxon id: | 1594222 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Elachistidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Gelechioidea;Depressariidae;Depressariinae;Agonopterix; |
| GoaT genome size (M): | 600 (ancestor) |
| GoaT asm span (M): | 545 (direct) |
| GoaT chr no.: | 60 (ancestor) |
| GoaT haploid no.: | 30 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilAgoAren |
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 |
|---|---|---|---|---|---|---|
| ilAgoAren1 | Ox000961 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA8603671 | SAMEA8603192 |
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 | ilAgoAren1 | 31 | 39.36 | 621,818,102 | 40.85 | 0.76 | 98.35 | 0.44 |   histogram.txt |
| pacbio | ilAgoAren1 | 31 | 21.19 | 539,434,266 | 28.72 | 0.76 | 98.76 | 0.15 |   histogram.txt |
| hic-arima2 | ilAgoAren1 | 31 | 33.25 | 1,471,022,192 | 54.50 | 1.81 | 98.14 | 0.43 |   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 | ilAgoAren1 | 2021-05-27 | 82781 | m64222e_210527_123147 | A01 | 1003 | 13,292,710,673 | 13,736 | SAMEA8603671 | ERR6939288 | |
| PacBio - HiFi | ilAgoAren1 | 2021-09-06 | 86243 | m64230e_210906_121446 | C01 | 1003 | 10,724,244,558 | 13,097 | SAMEA8603671 | ERR6909091 |
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 | ilAgoAren1 | 2021-06-28 | 38911_1#31 | 133,891,420 | 20,217,604,420 | SAMEA8603671 | ERR6787434 | qc complete | Agonopterix arenella (1.00) |
| Chromium genome | ilAgoAren1 | 2021-06-28 | 38911_1#30 | 117,226,348 | 17,701,178,548 | SAMEA8603671 | ERR6787433 | qc complete | Agonopterix arenella (1.00) |
| Chromium genome | ilAgoAren1 | 2021-06-28 | 38911_1#29 | 150,642,138 | 22,746,962,838 | SAMEA8603671 | ERR6787432 | qc complete | Agonopterix arenella (1.00) |
| Chromium genome | ilAgoAren1 | 2021-06-28 | 38911_1#32 | 110,380,698 | 16,667,485,398 | SAMEA8603671 | ERR6787435 | qc complete | Agonopterix arenella (1.00) |
| Hi-C - Arima v2 | ilAgoAren1 | 2021-06-04 | 38212_3#3 | 915,572,538 | 138,251,453,238 | SAMEA8603671 | ERR6787431 | qc complete | Agonopterix arenella (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 |
|---|---|
| 0.910933 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.901381 | [61 seqs] NZ_JTET01000001.1 Hafnia alvei strain DSM 30098 contig_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 |
|---|---|---|---|
| ilAgoAren1 | ptg000052l | 1899 |
|
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 |
|---|---|
| ilAgoAren1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ilAgoAren1 | hicanu.purging | 2021-09-09 | 15,166,790 | 127 | 545,567,112 | C:99.2%[S:98.5%,D:0.7%],F:0.4%,M:0.4%,n:1367 | Q58.4-C97.0(10X) | ||
| ilAgoAren1 | hicanu | 2021-09-09 | 2,378,788 | 1,777 | 1,114,197,172 | C:99.3%[S:64.4%,D:34.9%],F:0.4%,M:0.3%,n:1367 | Q46.0-C97.0(10X) | ||
| ilAgoAren1 | hifiasm.purging | 2021-09-09 | 19,442,860 | 38 | 556,583,265 | C:98.9%[S:97.7%,D:1.2%],F:0.4%,M:0.7%,n:1367 | Q61.6-C96.9(10X) | ||
| ilAgoAren1 | hifiasm.scaff.salsa | 2021-09-09 | 18,923,089 | 42 | 19,320,960 | 39 | 556,582,085 | - | |
| ilAgoAren1 | hifiasm | 2021-09-09 | 19,442,860 | 67 | 557,702,455 | C:98.9%[S:97.7%,D:1.2%],F:0.4%,M:0.7%,n:1367 | Q59.1-C97.0(10X) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilAgoAren1 | mitohifi.hicanu | mito | 2021-09-09 | 15,299 | 37 | None | MH473596.1; 15,539 bp; 37 genes | |
| ilAgoAren1 | mitohifi.reads | mito | 2021-09-09 | 15,315 | 36 | ND1;ND2;ND3 | MH473596.1; 15,539 bp; 37 genes | |
| ilAgoAren1 | mitohifi.hifiasm | mito | 2021-09-09 | 15,298 | 37 | None | MH473596.1; 15,539 bp; 37 genes |
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