Uloborus plumipes
Info
| NCBI taxon id: | 94033 NCBI; ENA; GoaT |
|---|---|
| Order: | Araneae |
| Family: | Uloboridae |
| NCBI lineage: | Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;Araneomorphae;Entelegynae;Deinopoidea;Uloboridae;Uloborus; |
| GoaT genome size (M): | 2,484 (ancestor) |
| GoaT asm span (M): | 2,151 (ancestor) |
| GoaT chr no.: | 22 (ancestor) |
| GoaT haploid no.: | 11 (ancestor) |
| GoaT ploidy: | 6 (ancestor) |
| ToLID prefix: | qqUloPlum |
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 |
|---|---|---|---|---|---|---|
| qqUloPlum1 | NHMUK014449139 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA8534515 | SAMEA8534438 |
| qqUloPlum1 | NHMUK014449139 | NATURAL HISTORY MUSEUM | FEMALE | HEAD | SAMEA8534515 | SAMEA8534438 |
| qqUloPlum2 | NHMUK014449140 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA8534516 | SAMEA8534439 |
| qqUloPlum2 | NHMUK014449140 | NATURAL HISTORY MUSEUM | FEMALE | HEAD | SAMEA8534516 | SAMEA8534439 |
| qqUloPlum3 | NHMUK014449141 | NATURAL HISTORY MUSEUM | FEMALE | THORAX | SAMEA8534517 | SAMEA8534440 |
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 | qqUloPlum3 | 31 | 15.29 | 256,050,252 | 84.27 | 5.86 | 69.14 | 2.42 |   histogram.txt |
| hic-arima2 | qqUloPlum5 | 31 | 30.25 | 718,257,861 | 69.48 | 4.01 | 95.71 | 0.92 |   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 | qqUloPlum3 | 2021-07-11 | 84271 | m64174e_210711_072508 | C01 | 1022 | 16,790,334,084 | 7,540 | SAMEA8534517 |
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 | qqUloPlum5 | 2022-03-15 | 44111_1#1 | 478,328,754 | 72,227,641,854 | SAMEA8534519 | qc complete | Uloborus plumipes (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 |
|---|---|
| 0.963095 | [256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...] |
| 0.936296 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.914483 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.91391 | [43 seqs] NZ_JQAM01000001.1 Wolbachia pipientis strain wRec s1, whole genome shotgun sequence [...] |
| 0.91333 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.911847 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.910625 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.908727 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.904322 | [157 seqs] NZ_LSYX01000001.1 Wolbachia endosymbiont of Dactylopius coccus strain wDacA Contig_1, whole genome shotgun sequence [...] |
| 0.904322 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, 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 |
|---|---|
| qqUloPlum3 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| No matching records found | ||||||||
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