Acleris sparsana
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Info
| NCBI taxon id: | 758717 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Tortricidae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Tortricoidea;Tortricidae;Tortricinae;Acleris; |
| GoaT genome size (M): | 600 (ancestor) |
| GoaT asm span (M): | 589 (direct) |
| GoaT chr no.: | 30 (ancestor) |
| GoaT haploid no.: | 30 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilAclSpar |
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 |
|---|---|---|---|---|---|---|
| ilAclSpar1 | Ox000978 | UNIVERSITY OF OXFORD | NOT_COLLECTED | WHOLE_ORGANISM | SAMEA8603760 | SAMEA8603209 |
| ilAclSpar2 | NHMUK013698321 | NATURAL HISTORY MUSEUM | MALE | THORAX | SAMEA14448896 | SAMEA14448454 |
| ilAclSpar2 | NHMUK013698321 | NATURAL HISTORY MUSEUM | MALE | HEAD | SAMEA14448896 | SAMEA14448454 |
| ilAclSpar2 | NHMUK013698321 | NATURAL HISTORY MUSEUM | MALE | ABDOMEN | SAMEA14448897 | SAMEA14448454 |
| ilAclSpar3 | NHMUK013698508 | NATURAL HISTORY MUSEUM | MALE | WHOLE_ORGANISM | SAMEA114806193 | SAMEA114805993 |
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 | ilAclSpar1 | 31 | 38.19 | 637,422,377 | 36.48 | 1.53 | 98.13 | 0.41 |   histogram.txt |
| pacbio | ilAclSpar1 | 31 | 18.68 | 584,449,850 | 28.27 | 1.42 | 99.07 | 0.19 |   histogram.txt |
| hic-arima2 | ilAclSpar1 | 31 | 17.29 | 1,466,203,157 | 54.06 | 3.14 | 97.22 | 0.62 |   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 | ilAclSpar1 | 2021-06-05 | 82995 | m64230e_210605_175953 | B01 | 1022 | 23,186,565,141 | 15,810 | SAMEA8603760 | ERR6808046 |
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 | ilAclSpar1 | 2021-06-28 | 38911_1#26 | 117,890,106 | 17,801,406,006 | SAMEA8603760 | ERR6688756 | qc complete | Acleris sparsana (1.00) |
| Chromium genome | ilAclSpar1 | 2021-06-28 | 38911_1#25 | 164,843,350 | 24,891,345,850 | SAMEA8603760 | ERR6688755 | qc complete | Acleris sparsana (1.00) |
| Chromium genome | ilAclSpar1 | 2021-06-28 | 38911_1#27 | 54,886,806 | 8,287,907,706 | SAMEA8603760 | ERR6688757 | qc complete | Acleris sparsana (1.00) |
| Chromium genome | ilAclSpar1 | 2021-06-28 | 38911_1#28 | 168,256,764 | 25,406,771,364 | SAMEA8603760 | ERR6688758 | qc complete | Acleris sparsana (1.00) |
| Hi-C - Arima v2 | ilAclSpar1 | 2021-06-04 | 38212_3#2 | 504,294,566 | 76,148,479,466 | SAMEA8603760 | ERR6688754 | qc complete | Acleris sparsana (1.00) |
| RNA PolyA | ilAclSpar2 | 2022-09-29 | 45898_4#3 | 93,983,544 | 14,191,515,144 | SAMEA14448896 | ERR10377998 | qc complete | Acleris sparsana (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 |
|---|---|
| 0.920352 | 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 |
|---|---|---|---|
| ilAclSpar1 | ptg000037l | 1904 |
|
| ilAclSpar1 | ptg000054l | 2198 |
|
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 | ||
| ilAclSpar1 | Trypanosomatidae | 3,909 | 0 | C:46.2%[S:40.8%,D:5.4%],F:6.2%,M:47.6%,n:130 | C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:130 | 1 | 0.02Mb | 37 | C:0.8%[S:0.8%,D:0.0%],F:0.0%,M:99.2%,n:130 | 3 | 0.08Mb | 20 |
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| ilAclSpar1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| ilAclSpar1 | hicanu.purging | 2021-08-21 | 12,329,209 | 101 | 587,738,602 | C:98.7%[S:98.2%,D:0.5%],F:0.5%,M:0.8%,n:1367 | Q56.8-C97.7(10X) | ||
| ilAclSpar1 | hicanu | 2021-08-21 | 8,113,671 | 1,505 | 1,199,835,058 | C:99.1%[S:57.8%,D:41.3%],F:0.5%,M:0.4%,n:1367 | Q45.3-C97.7(10X) | ||
| ilAclSpar1 | hifiasm.purging | 2021-08-21 | 18,942,159 | 43 | 589,575,269 | C:98.7%[S:98.0%,D:0.7%],F:0.4%,M:0.9%,n:1367 | Q56.9-C97.7(10X) | ||
| ilAclSpar1 | hifiasm.scaff.salsa | 2021-08-21 | 18,942,093 | 43 | 19,007,631 | 37 | 589,576,359 | - | |
| ilAclSpar1 | hifiasm | 2021-08-21 | 18,942,159 | 87 | 592,282,519 | C:98.7%[S:98.0%,D:0.7%],F:0.4%,M:0.9%,n:1367 | Q56.4-C97.7(10X) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilAclSpar1 | mitohifi.reads | mito | 2021-08-21 | 16,373 | 36 | None | True | MW924665.1; 15,558 bp; 37 genes |
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