Orobanche hederae
Info
| NCBI taxon id: | 79235 NCBI; ENA; GoaT |
|---|---|
| Order: | Lamiales |
| Family: | Orobanchaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;asterids;lamiids;Lamiales;Orobanchaceae;Orobancheae;Orobanche; |
| GoaT genome size (M): | 2,767 (direct) |
| GoaT asm span (M): | 3,648 (ancestor) |
| GoaT chr no.: | 38 (direct) |
| GoaT haploid no.: | 19 (direct) |
| GoaT ploidy: | 2 (direct) |
| ToLID prefix: | daOroHede |
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 |
|---|---|---|---|---|---|---|
| daOroHede1 | KDTOL10004 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521803 | SAMEA7521713 |
| daOroHede1 | KDTOL10004 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521802 | SAMEA7521713 |
| daOroHede1 | KDTOL10004 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521804 | SAMEA7521713 |
| daOroHede2 | KDTOL10005 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521805 | SAMEA7521714 |
| daOroHede2 | KDTOL10005 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7521807 | SAMEA7521714 |
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 | daOroHede2 | 31 | 45.38 | 1,312,607,130 | 71.24 | 11.72 | 86.34 | 0.08 |   histogram.txt |
| hic-arima2 | daOroHede2 | 31 | 74.35 | 2,060,055,553 | 68.51 | 0.84 | 95.95 | 0.38 |   histogram.txt |
| pacbio | daOroHede1 | 31 | 15.71 | 770,404,281 | 83.31 | 5.69 | 77.20 | 0.70 |   histogram.txt |
| 10x | daOroHede1 | 31 | 40.49 | 1,292,170,946 | 71.86 | 9.17 | 86.29 | 0.41 |   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 | daOroHede1 | 2021-04-18 | 81442 | m64221e_210418_225721 | C01 | 1021 | 9,188,559,649 | 13,035 | SAMEA7521802 | ||
| PacBio - HiFi | daOroHede1 | 2021-07-26 | 84817 | m64174e_210726_181748 | D01 | 1021 | 1,598,108,492 | 12,396 | SAMEA7521802 | ||
| PacBio - HiFi (ULI) | daOroHede1 | 2023-06-30 | TRACTION-RUN-655 | m64178e_230630_035715 | D01 | 1015 | 19,398,309,699 | 8,514 | SAMEA7521802 | ||
| PacBio - HiFi | daOroHede2 | 2023-10-07 | TRACTION-RUN-878 | m84098_231007_113932_s4 | D01 | 2059 | 50,941,098,743 | 14,945 | SAMEA7521805 | ||
| PacBio - HiFi | daOroHede2 | 2024-04-30 | TRACTION-RUN-1260 | m84093_240430_114929_s4 | D01 | 2079 | 19,884,682,220 | 13,836 | SAMEA7521805 | ||
| PacBio - HiFi | daOroHede2 | 2024-05-21 | TRACTION-RUN-1296 | m84098_240521_103850_s2 | B01 | 2008 | 51,530,224,886 | 12,932 | SAMEA7521805 |
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 | daOroHede2 | 2023-08-01 | 47676_1#2 | 2,850,494,540 | 430,424,675,540 | SAMEA7521806 | qc complete | Orobanche hederae (1.00) | |
| Chromium genome | daOroHede1 | 2021-06-01 | 37642_1#14 | 267,286,664 | 40,360,286,264 | SAMEA7521802 | qc complete | Orobanche hederae (1.00) | |
| Chromium genome | daOroHede1 | 2021-06-01 | 37642_1#15 | 290,744,450 | 43,902,411,950 | SAMEA7521802 | qc complete | Orobanche hederae (1.00) | |
| Chromium genome | daOroHede1 | 2021-06-01 | 37642_1#16 | 247,622,736 | 37,391,033,136 | SAMEA7521802 | qc complete | Orobanche hederae (1.00) | |
| Chromium genome | daOroHede1 | 2021-06-01 | 37642_1#13 | 280,848,072 | 42,408,058,872 | SAMEA7521802 | qc complete | Orobanche hederae (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 |
|---|---|
| 0.957646 | [124 seqs] NZ_ACNO01000124.1 Rhodococcus erythropolis SK121 contig00004, whole genome shotgun sequence [...] |
| 0.918041 | NZ_CP013290.1 Janibacter terrae strain YFY001, complete genome |
| 0.900615 | [833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...] |
| 0.900227 | 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 |
|---|---|---|---|
| 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 |
|---|---|
| daOroHede1 |    |
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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