Abraxas sylvata
clouded magpie
Info
| NCBI taxon id: | 190335 NCBI; ENA; GoaT |
|---|---|
| Order: | Lepidoptera |
| Family: | Geometridae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Abraxas; |
| GoaT genome size (M): | 831 (ancestor) |
| GoaT asm span (M): | 491 (ancestor) |
| GoaT chr no.: | 56 (ancestor) |
| GoaT haploid no.: | 27 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | ilAbrSylv |
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 |
|---|---|---|---|---|---|---|
| ilAbrSylv1 | SAN00002578 | SANGER INSTITUTE | NOT_COLLECTED | **OTHER_SOMATIC_ANIMAL_TISSUE** | SAMEA112198478 | SAMEA112198460 |
| ilAbrSylv1 | SAN00002578 | SANGER INSTITUTE | NOT_COLLECTED | THORAX | SAMEA112198476 | SAMEA112198460 |
| ilAbrSylv1 | SAN00002578 | SANGER INSTITUTE | NOT_COLLECTED | ABDOMEN | SAMEA112198477 | SAMEA112198460 |
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 | ilAbrSylv1 | 31 | 22.46 | 453,815,860 | 26.94 | 0.44 | 98.53 | 0.15 |   histogram.txt |
| hic-arima2 | ilAbrSylv1 | 31 | 113.1 | 470,590,279 | 37.68 | 4.69 | 93.22 | 0.20 |   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 | ilAbrSylv1 | 2023-03-10 | TRACTION-RUN-490 | m64229e_230310_174556 | B01 | 1020 | 21,391,759,266 | 13,321 | SAMEA112198476 | ERR12370385 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| Hi-C - Arima v2 | ilAbrSylv1 | 2024-02-02 | 48375_4#2 | 936,083,984 | 141,348,681,584 | SAMEA112198478 | qc complete | Abraxas sylvata (1.00) | |
| RNA PolyA | ilAbrSylv1 | 2023-11-02 | 48017_1#79 | 57,512,538 | 8,684,393,238 | SAMEA112198478 | ERR12374377 | qc complete | Abraxas sylvata (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 |
|---|---|
| 0.922314 | 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 |
|---|---|---|---|
| ilAbrSylv1 | ptg000002l | 1898 |
|
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 |
|---|---|
| No matching records found | |
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
ilAbrSylv1.hifiasm.20240202
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| ilAbrSylv1 | hifiasm-hic | 2024-02-02 | 6,791,315 | 229 | 444,092,191 | C:95.8%[S:95.2%,D:0.6%],F:0.4%,M:3.8%,n:1367 | Q64.8-C99.4(HiFi) | ||
| ilAbrSylv1 | hifiasm-hic | 2024-02-02 | 9,400,240 | 222 | 472,348,324 | - | |||
| ilAbrSylv1 | hifiasm-hic.scaffolding_hap2.yahs | 2024-02-02 | 5,874,572 | 264 | 16,116,877 | 167 | 461,346,242 | C:98.5%[S:96.6%,D:1.9%],F:0.3%,M:1.2%,n:1367 | Q64.2-C99.4(HiFi) |
| ilAbrSylv1 | hifiasm-hic.scaffolding_hap1.yahs | 2024-02-02 | 6,754,908 | 244 | 16,009,052 | 151 | 444,110,791 | C:95.6%[S:95.1%,D:0.5%],F:0.4%,M:4.0%,n:1367 | Q64.8-C99.4(HiFi) |
| ilAbrSylv1 | hifiasm-hic.purging | 2024-02-02 | 6,851,776 | 135 | 435,285,116 | C:95.7%[S:95.2%,D:0.5%],F:0.4%,M:3.9%,n:1367 | Q65.4-C99.3(HiFi) | ||
| ilAbrSylv1 | hifiasm-hic | 2024-02-02 | 6,485,448 | 243 | 461,326,842 | C:98.5%[S:96.6%,D:1.9%],F:0.3%,M:1.2%,n:1367 | - | ||
| ilAbrSylv1 | hifiasm.purging | 2024-02-02 | 10,912,184 | 97 | 463,363,771 | C:98.8%[S:97.8%,D:1.0%],F:0.4%,M:0.8%,n:1367 | Q64.6-C99.4(HiFi) | ||
| ilAbrSylv1 | hifiasm | 2024-02-02 | 9,418,848 | 217 | 472,391,915 | C:98.9%[S:97.3%,D:1.6%],F:0.3%,M:0.8%,n:1367 | Q63.4-C99.4(HiFi) | ||
| ilAbrSylv1 | hifiasm.scaffolding.yahs | 2024-02-02 | 8,127,816 | 128 | 16,301,245 | 64 | 463,376,571 | C:98.9%[S:97.9%,D:1.0%],F:0.4%,M:0.7%,n:1367 | Q64.6-C99.4(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| ilAbrSylv1 | mitohifi.hifiasm-hic | mito | 2024-02-02 | 15,741 | 35 | None | True | NC_034804.1; 15,537 bp; 37 genes |
| ilAbrSylv1 | mitohifi.hifiasm | mito | 2024-02-02 | 15,741 | 35 | None | True | NC_034804.1; 15,537 bp; 37 genes |
| ilAbrSylv1 | mitohifi.reads | mito | 2024-02-02 | 15,753 | 37 | COX3;ND4L;ND3 | True | NC_034804.1; 15,537 bp; 37 genes |
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