Linaria vulgaris
common toadflax
Info
| NCBI taxon id: | 43171 NCBI; ENA; GoaT |
|---|---|
| Order: | Lamiales |
| Family: | Plantaginaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;asterids;lamiids;Lamiales;Plantaginaceae;Antirrhineae;Linaria; |
| GoaT genome size (M): | 938 (direct) |
| GoaT asm span (M): | 759 (direct) |
| GoaT chr no.: | 12 (direct) |
| GoaT haploid no.: | 4 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | daLinVulg |
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 |
|---|---|---|---|---|---|---|
| daLinVulg1 | KDTOL10067 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522347 | SAMEA7522288 |
| daLinVulg1 | KDTOL10067 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522343 | SAMEA7522288 |
| daLinVulg1 | KDTOL10067 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | FLOWER | SAMEA7522341 | SAMEA7522288 |
| daLinVulg1 | KDTOL10067 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522344 | SAMEA7522288 |
| daLinVulg1 | KDTOL10067 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522345 | SAMEA7522288 |
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 | daLinVulg1 | 31 | 13.86 | 831,725,333 | 48.80 | 1.81 | 96.87 | 0.24 |   histogram.txt |
| hic-arima2 | daLinVulg1 | 31 | 62.76 | 692,025,822 | 53.85 | 3.09 | 91.53 | 0.51 |   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 | daLinVulg1 | 2021-02-12 | 79754 | m64097e_210212_154319 | A01 | 1003 | 4,833,995,903 | 13,579 | SAMEA7522343 | ERR8705859 | |
| PacBio - HiFi | daLinVulg1 | 2021-05-27 | 82794 | m64097e_210527_163220 | A01 | 1018 | 20,027,769,805 | 15,381 | SAMEA7522347 | ERR8705860 |
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 | daLinVulg1 | 2021-08-16 | 40063_3#2 | 840,213,430 | 126,872,227,930 | SAMEA7522347 | ERR8702786 | qc complete | Linaria vulgaris (1.00) |
| RNA PolyA | daLinVulg1 | 2022-09-29 | 45898_4#17 | 58,465,058 | 8,828,223,758 | SAMEA7522340 | ERR10378005 | qc complete | Linaria vulgaris (1.00) |
| RNA PolyA | daLinVulg1 | 2022-09-29 | 45898_4#8 | 71,329,826 | 10,770,803,726 | SAMEA7522341 | ERR10378004 | qc complete | Linaria vulgaris (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 |
|---|---|
| 0.913038 | 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 |
|---|---|---|---|
| daLinVulg1 | atg000137l | 1495 |
|
| daLinVulg1 | atg000253l | 579 |
|
| daLinVulg1 | atg000415l | 1482 |
|
| daLinVulg1 | ptg000010l | 1099 |
|
| daLinVulg1 | ptg000014l | 1477 |
|
| daLinVulg1 | ptg000032l | 1486 |
|
| daLinVulg1 | ptg000034l | 1433 |
|
| daLinVulg1 | ptg000041l | 1495 |
|
| daLinVulg1 | ptg000046l | 1806 |
|
| daLinVulg1 | ptg000114l | 1488 |
|
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 |
|---|---|
| daLinVulg1 |    |
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
daLinVulg1.hifiasm.20220209
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| daLinVulg1 | hifiasm.purging | 2022-02-09 | 12,652,593 | 189 | 787,217,471 | C:97.2%[S:92.0%,D:5.2%],F:0.6%,M:2.2%,n:2326 | Q61.7-C97.7(HiFi) | ||
| daLinVulg1 | hifiasm | 2022-02-09 | 12,050,218 | 1,111 | 851,658,774 | C:97.1%[S:90.4%,D:6.7%],F:0.6%,M:2.3%,n:2326 | Q60.0-C97.9(HiFi) | ||
| daLinVulg1 | hifiasm.scaffolding.salsa | 2022-02-09 | 12,652,593 | 200 | 122,127,207 | 136 | 787,249,471 | C:97.2%[S:92.2%,D:5.0%],F:0.6%,M:2.2%,n:2326 | Q61.7-C97.7(HiFi) |
| daLinVulg1 | hifiasm.scaffolding.yahs | 2022-02-09 | 12,476,000 | 221 | 154,963,983 | 137 | 787,234,271 | C:97.2%[S:92.2%,D:5.0%],F:0.6%,M:2.2%,n:2326 | Q61.7-C97.7(HiFi) |
| daLinVulg1 | hicanu | 2022-02-09 | 1,808,346 | 6,046 | 1,638,419,577 | C:97.7%[S:2.9%,D:94.8%],F:0.4%,M:1.9%,n:2326 | Q63.4-C98.0(HiFi) | ||
| daLinVulg1 | hicanu.purging | 2022-02-09 | 2,811,853 | 700 | 849,799,773 | C:97.2%[S:84.8%,D:12.4%],F:0.6%,M:2.2%,n:2326 | Q63.8-C97.8(HiFi) |
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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