Actinia fragacea
strawberry beadlet anemone
Info
| NCBI taxon id: | 396334 NCBI; ENA; GoaT |
|---|---|
| Order: | Actiniaria |
| Family: | Actiniidae |
| NCBI lineage: | Eukaryota;Metazoa;Cnidaria;Anthozoa;Hexacorallia;Actiniaria;Actiniidae;Actinia; |
| GoaT genome size (M): | 508 (ancestor) |
| GoaT asm span (M): | 323 (ancestor) |
| GoaT chr no.: | 18 (ancestor) |
| GoaT haploid no.: | 6 (ancestor) |
| GoaT ploidy: | 12 (ancestor) |
| ToLID prefix: | jaActFrag |
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 |
|---|---|---|---|---|---|---|
| jaActFrag1 | SAN0000176 | SANGER INSTITUTE | NOT_COLLECTED | BODYWALL | SAMEA7523186 | SAMEA7523098 |
| jaActFrag1 | SAN0000176 | SANGER INSTITUTE | NOT_COLLECTED | BODYWALL | SAMEA7523180 | SAMEA7523098 |
| jaActFrag1 | SAN0000176 | SANGER INSTITUTE | NOT_COLLECTED | BODYWALL | SAMEA7523184 | SAMEA7523098 |
| jaActFrag1 | SAN0000176 | SANGER INSTITUTE | NOT_COLLECTED | BODYWALL | SAMEA7523183 | SAMEA7523098 |
| jaActFrag1 | SAN0000176 | SANGER INSTITUTE | NOT_COLLECTED | BODYWALL | SAMEA7523182 | SAMEA7523098 |
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 | jaActFrag1 | 31 | 48.86 | 362,759,005 | 46.68 | 1.65 | 94.33 | 0.12 |   histogram.txt |
| hic-arima2 | jaActFrag1 | 31 | 81.38 | 526,968,171 | 66.05 | 2.13 | 95.42 | 0.56 |   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 | jaActFrag1 | 2020-11-29 | 78601 | m64125_201129_130643 | D01 | 1009 | 3,994,431,191 | 7,642 | SAMEA7523181 | ||
| PacBio - HiFi | jaActFrag1 | 2024-09-09 | TRACTION-RUN-1489 | m84098_240909_112906_s3 | C01 | 2024 | 32,880,281,656 | 10,508 | SAMEA7523183 |
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 | jaActFrag1 | 2020-11-04 | 35312_4#1 | 841,951,334 | 127,134,651,434 | SAMEA7523181 | qc complete | Urticina felina (1.00) | |
| RNA PolyA | jaActFrag1 | 2021-03-19 | 36703_5#12 | 48,058,624 | 7,256,852,224 | SAMEA7523187 | qc complete | Urticina felina (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 |
|---|---|
| 0.962588 | [436 seqs] NZ_MKCO01000001.1 Epsilonproteobacteria bacterium LFT 1.7 Contig1, whole genome shotgun sequence [...] |
| 0.930838 | [183 seqs] NZ_AJZF02000001.1 Vibrio splendidus ZF-90 ZF-90_contig_0, whole genome shotgun sequence [...] |
| 0.912148 | 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 |
|---|---|---|---|
| jaActFrag1 | ptg000082l | 1514 |
|
| jaActFrag1 | ptg000141l | 1800 |
|
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 | ||
| jaActFrag1 | Arcobacteraceae | 1,387 | 0.03 | C:78.1%[S:33.0%,D:45.1%],F:4.6%,M:17.3%,n:628 | C:2.1%[S:2.1%,D:0.0%],F:0.6%,M:97.3%,n:628 | 3 | 0.08Mb | 27 | C:1.0%[S:1.0%,D:0.0%],F:0.0%,M:99.0%,n:628 | 2 | 0.06Mb | 23 |
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| jaActFrag1 |    |
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
jaActFrag1.hifiasm.20240913
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| jaActFrag1 | hifiasm-hic.purging | 2024-09-13 | 7,781,757 | 139 | 381,098,110 | C:94.7%[S:93.8%,D:0.9%],F:1.8%,M:3.5%,n:954 | Q64.4-C98.6(HiFi) | ||
| jaActFrag1 | hifiasm-hic.scaffolding_hap1.yahs | 2024-09-13 | 6,737,736 | 408 | 14,588,779 | 326 | 393,148,482 | C:94.9%[S:93.6%,D:1.3%],F:1.8%,M:3.3%,n:954 | Q62.5-C99.4(HiFi) |
| jaActFrag1 | hifiasm-hic.scaffolding_hap2.yahs | 2024-09-13 | 5,619,000 | 386 | 12,534,356 | 297 | 462,016,584 | C:96.2%[S:93.7%,D:2.5%],F:1.7%,M:2.1%,n:954 | Q64.3-C99.4(HiFi) |
| jaActFrag1 | hifiasm-hic.hap2 | 2024-09-13 | 7,319,467 | 274 | 461,998,784 | C:96.3%[S:93.8%,D:2.5%],F:1.6%,M:2.1%,n:954 | Q64.3-C99.4(HiFi) | ||
| jaActFrag1 | hifiasm-hic.hap1 | 2024-09-13 | 7,781,757 | 345 | 393,132,082 | C:94.8%[S:93.5%,D:1.3%],F:1.8%,M:3.4%,n:954 | Q62.5-C99.4(HiFi) | ||
| jaActFrag1 | hifiasm.purging | 2024-09-13 | 13,629,599 | 72 | 439,269,470 | C:96.2%[S:94.9%,D:1.3%],F:1.9%,M:1.9%,n:954 | Q64.0-C99.2(HiFi) | ||
| jaActFrag1 | hifiasm.scaffolding.yahs | 2024-09-13 | 9,695,648 | 146 | 14,987,051 | 114 | 439,275,870 | C:96.3%[S:95.0%,D:1.3%],F:1.9%,M:1.8%,n:954 | Q64.0-C99.2(HiFi) |
| jaActFrag1 | hifiasm | 2024-09-13 | 13,188,249 | 194 | 457,791,057 | C:96.2%[S:94.7%,D:1.5%],F:1.9%,M:1.9%,n:954 | Q62.8-C99.4(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| jaActFrag1 | mitohifi.reads | mito | 2023-12-16 | 20,481 | 29 | None | True | 1 | NC_044902.1; 20,691 bp; 17 genes |
| jaActFrag1 | mitohifi.hifiasm-hic | mito | 2024-09-13 | 19,857 | 28 | None | False | 1 | NC_044902.1; 20,691 bp; 17 genes |
| jaActFrag1 | mitohifi.reads | mito | 2024-09-13 | 20,481 | 29 | None | True | 1 | NC_044902.1; 20,691 bp; 17 genes |
| jaActFrag1 | mitohifi.hifiasm | mito | 2024-09-13 | 20,481 | 29 | None | False | 1 | NC_044902.1; 20,691 bp; 17 genes |
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