Atropa belladonna
belladonna
Info
| NCBI taxon id: | 33113 NCBI; ENA; GoaT |
|---|---|
| Order: | Solanales |
| Family: | Solanaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;asterids;lamiids;Solanales;Solanaceae;Solanoideae;Hyoscyameae;Atropa; |
| GoaT genome size (M): | 2,122 (direct) |
| GoaT asm span (M): | 2,145 (ancestor) |
| GoaT chr no.: | 72 (direct) |
| GoaT haploid no.: | 30 (direct) |
| GoaT ploidy: | 6 (direct) |
| ToLID prefix: | daAtrBela |
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 |
|---|---|---|---|---|---|---|
| daAtrBela1 | KDTOL10009 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521846 | SAMEA7521818 |
| daAtrBela1 | KDTOL10009 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521848 | SAMEA7521818 |
| daAtrBela1 | KDTOL10009 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | FLOWER | SAMEA7521851 | SAMEA7521818 |
| daAtrBela1 | KDTOL10009 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521844 | SAMEA7521818 |
| daAtrBela1 | KDTOL10009 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521850 | SAMEA7521818 |
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 | daAtrBela1 | 31 | 12.19 | 1,795,781,358 | 32.24 | 0.16 | 98.53 | 0.13 |   histogram.txt |
| 10x | daAtrBela1 | 31 | 50.3 | 940,201,805 | 35.53 | 22.86 | 95.30 | 0.34 |   histogram.txt |
| hic-arima2 | daAtrBela1 | 31 | 30.9 | 2,454,484,584 | 0.00 | 100.00 | 6.72 | 0.12 |   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 | daAtrBela1 | 2021-01-16 | 79175 | m64089_210116_170713 | C01 | 1001 | 25,313,175,987 | 11,890 | SAMEA7521850 | ||
| PacBio - HiFi | daAtrBela1 | 2021-01-30 | 79445 | m64178e_210130_103148 | C01 | 1001 | 20,324,124,846 | 11,582 | SAMEA7521850 |
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 | daAtrBela1 | 2021-03-25 | 37020_1#23 | 177,928,824 | 26,867,252,424 | SAMEA7521847 | qc complete | Atropa belladonna (1.00) | |
| Chromium genome | daAtrBela1 | 2021-03-25 | 37020_1#21 | 268,765,956 | 40,583,659,356 | SAMEA7521847 | qc complete | Atropa belladonna (1.00) | |
| Chromium genome | daAtrBela1 | 2021-03-25 | 37020_1#24 | 176,733,376 | 26,686,739,776 | SAMEA7521847 | qc complete | Atropa belladonna (1.00) | |
| Chromium genome | daAtrBela1 | 2021-03-25 | 37020_1#22 | 334,839,444 | 50,560,756,044 | SAMEA7521847 | qc complete | Atropa belladonna (1.00) | |
| Hi-C - Arima v2 | daAtrBela1 | 2023-06-20 | 47489_1#2 | 1,303,122,314 | 196,771,469,414 | SAMEA7521844 | qc complete | Atropa belladonna (1.00) | |
| RNA PolyA | daAtrBela1 | 2023-09-19 | 47846_4#57 | 61,138,868 | 9,231,969,068 | SAMEA7521844 | qc complete | Atropa belladonna (1.00) | |
| RNA PolyA | daAtrBela1 | 2023-09-01 | 47797_1#36 | 23,818,726 | 3,596,627,626 | SAMEA7521844 | qc complete | Atropa belladonna (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 |
|---|---|
| 0.935218 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.909686 | NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome |
| 0.909049 | [28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...] |
| 0.909049 | NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome |
| 0.908727 | NC_019711.1 Enterobacteria phage HK629, complete genome |
| 0.905028 | [2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...] |
| 0.903242 | [3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...] |
| 0.903242 | [777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...] |
| 0.901759 | NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome |
| 0.901 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
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 |
|---|---|
| daAtrBela1 |    |
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 | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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