Alnus glutinosa
Info
| NCBI taxon id: | 3517 NCBI; ENA; GoaT |
|---|---|
| Order: | Fagales |
| Family: | Betulaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Fagales;Betulaceae;Alnus; |
| GoaT genome size (M): | 542 (direct) |
| GoaT asm span (M): | 456 (direct) |
| GoaT chr no.: | 28 (direct) |
| GoaT haploid no.: | 14 (direct) |
| GoaT ploidy: | 4 (direct) |
| ToLID prefix: | dhAlnGlut |
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 |
|---|---|---|---|---|---|---|
| dhAlnGlut1 | KDTOL10041 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522122 | SAMEA7522050 |
| dhAlnGlut1 | KDTOL10041 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522125 | SAMEA7522050 |
| dhAlnGlut1 | KDTOL10041 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522126 | SAMEA7522050 |
| dhAlnGlut1 | KDTOL10041 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522124 | SAMEA7522050 |
| dhAlnGlut1 | KDTOL10041 | ROYAL BOTANIC GARDENS KEW | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7522128 | SAMEA7522050 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| 10x | dhAlnGlut1 | 31 | 42.7 | 495,453,551 | 38.40 | 1.18 | 98.37 | 0.46 |   histogram.txt |
| pacbio | dhAlnGlut1 | 31 | 18.81 | 477,057,445 | 34.15 | 1.20 | 97.89 | 0.19 |   histogram.txt |
| hic-arima2 | dhAlnGlut1 | 31 | 39.5 | 681,280,903 | 60.88 | 0.41 | 97.57 | 0.53 |   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 | dhAlnGlut1 | 2021-02-05 | 79606 | m64016_210205_142724 | B01 | 1008 | 10,317,513,559 | 14,893 | SAMEA7522125 | ERR6808004 | |
| PacBio - HiFi | dhAlnGlut1 | 2021-06-15 | 83253 | m64089e_210615_171405 | D01 | 1002 | 8,759,632,537 | 15,036 | SAMEA7522127 | ERR6939242 |
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 | dhAlnGlut1 | 2021-02-15 | 36276_3#9 | 106,251,824 | 16,044,025,424 | SAMEA7522125 | ERR6688529 | qc complete | Alnus glutinosa (1.00) |
| Chromium genome | dhAlnGlut1 | 2021-02-15 | 36276_3#12 | 110,879,662 | 16,742,828,962 | SAMEA7522125 | ERR6688532 | qc complete | Alnus glutinosa (1.00) |
| Chromium genome | dhAlnGlut1 | 2021-02-15 | 36276_3#10 | 121,130,154 | 18,290,653,254 | SAMEA7522125 | ERR6688530 | qc complete | Alnus glutinosa (1.00) |
| Chromium genome | dhAlnGlut1 | 2021-02-15 | 36276_3#11 | 107,655,508 | 16,255,981,708 | SAMEA7522125 | ERR6688531 | qc complete | Alnus glutinosa (1.00) |
| Hi-C - Arima v2 | dhAlnGlut1 | 2021-05-04 | 37689_2#2 | 523,623,326 | 79,067,122,226 | SAMEA7522125 | ERR6688533 | qc complete | Alnus glutinosa (1.00) |
| RNA PolyA | dhAlnGlut2 | 2022-03-25 | 44268_5#2 | 44,705,048 | 6,750,462,248 | SAMEA7536056 | ERR9435007 | qc complete | Alnus glutinosa (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 |
|---|---|
| 0.920101 | 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 |
|---|---|
| dhAlnGlut1 |    |
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 |
|---|---|---|---|---|---|---|---|---|---|
| dhAlnGlut1 | hicanu.purging | 2021-06-18 | 5,447,591 | 320 | 467,580,971 | C:98.5%[S:94.5%,D:4.0%],F:0.5%,M:1.0%,n:2326 | Q51.3-C96.8(10X); Q53.1-C98.9(HiFi) | ||
| dhAlnGlut1 | hicanu | 2021-06-18 | 2,977,940 | 2,617 | 954,337,767 | C:98.7%[S:41.7%,D:57.0%],F:0.4%,M:0.9%,n:2326 | Q41.6-C96.8(10X); Q46.1-C99.0(HiFi) | ||
| dhAlnGlut1 | hifiasm | 2021-06-18 | 24,382,815 | 590 | 475,755,102 | C:98.6%[S:95.6%,D:3.0%],F:0.3%,M:1.1%,n:2326 | Q47.1-C96.8(10X); Q50.9-C99.0(HiFi) | ||
| dhAlnGlut1 | hifiasm.purging | 2021-06-18 | 24,382,815 | 149 | 458,516,533 | C:98.6%[S:95.6%,D:3.0%],F:0.3%,M:1.1%,n:2326 | Q50.7-C96.8(10X); Q52.7-C98.9(HiFi) | ||
| dhAlnGlut1 | hifiasm.scaff.salsa | 2021-06-18 | 24,382,369 | 149 | 30,489,098 | 133 | 458,516,209 | - |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| dhAlnGlut1 | oatk.reads | mito | 2021-06-18 | 661,083 | 58 | ccmFN;rps19;ATP6 | False | NC_065018.1; 573,177 bp; 60 genes |
| dhAlnGlut1 | oatk.reads | pltd | 2021-06-18 | 160,819 | 105 | rpl2;atpF | True | NC_039930.1; 160,770 bp; 130 genes |
| dhAlnGlut1 | oatk.reads | mito | 2021-06-18 | 661,083 | False | NC_065018.1; bp; 0 genes | ||
| dhAlnGlut1 | oatk.reads | pltd | 2021-06-18 | 160,819 | 105 | rpl2;atpF | True | NC_039930.1; 160,770 bp; 130 genes |
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