Crataegus monogyna
Hawthorn
Info
| NCBI taxon id: | 140997 NCBI; ENA; GoaT |
|---|---|
| Order: | Rosales |
| Family: | Rosaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Rosaceae;Amygdaloideae;Maleae;Crataegus; |
| GoaT genome size (M): | 743 (direct) |
| GoaT asm span (M): | 627 (ancestor) |
| GoaT chr no.: | 34 (direct) |
| GoaT haploid no.: | 17 (direct) |
| GoaT ploidy: | 3 (direct) |
| ToLID prefix: | drCraMono |
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 |
|---|---|---|---|---|---|---|
| drCraMono1 | KDTOL10193 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA9143977 | SAMEA9143089 |
| drCraMono1 | KDTOL10193 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA9143975 | SAMEA9143089 |
| drCraMono1 | KDTOL10193 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA9143972 | SAMEA9143089 |
| drCraMono1 | KDTOL10193 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA9143976 | SAMEA9143089 |
| drCraMono1 | KDTOL10193 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | FLOWER | SAMEA9143979 | SAMEA9143089 |
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 | drCraMono1 | 31 | 42.7 | 693,517,263 | 42.56 | 1.00 | 96.37 | 0.09 |   histogram.txt |
| hic-arima2 | drCraMono1 | 31 | 46.53 | 848,832,316 | 71.93 | 0.90 | 96.38 | 0.31 |   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 | drCraMono1 | 2021-08-27 | 85992 | m64094e_210827_212853 | B01 | 1018 | 6,131,279,940 | 12,725 | SAMEA9143972 | ||
| PacBio - HiFi | drCraMono1 | 2024-03-01 | TRACTION-RUN-1154 | m84047_240301_122836_s3 | C01 | 2017 | 54,940,292,141 | 16,153 | SAMEA9143973 |
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 | drCraMono1 | 2022-01-10 | 42852_1#7 | 719,966,736 | 108,714,977,136 | SAMEA9143973 | qc complete | Crataegus monogyna (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 |
|---|---|
| 0.909686 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.907748 | [2182 seqs] NW_008988039.1 Pyrus x bretschneideri cultivar Dangshansuli unplaced genomic scaffold, Pbr_v1.0 scaffold1.0.1, whole genome shotgun sequence [...] |
| 0.906067 | [1251 seqs] NC_024239.1 Malus x domestica cultivar Golden Delicious chromosome 1, MalDomGD1.0 Primary Assembly, 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 |
|---|---|
| drCraMono1 |    |
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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