Sthenelais limicola
(A segmented worm)
Info
| NCBI taxon id: | 1210413 NCBI; ENA; GoaT |
|---|---|
| Order: | Phyllodocida |
| Family: | Sigalionidae |
| NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Annelida;Polychaeta;Errantia;Phyllodocida;Sigalionidae;Sthenelais; |
| GoaT genome size (M): | 1,486 (ancestor) |
| GoaT asm span (M): | 1,131 (direct) |
| GoaT chr no.: | 26 (ancestor) |
| GoaT haploid no.: | 12 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | wpSthLimi |
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 |
|---|---|---|---|---|---|---|
| wpSthLimi1 | MBA-201117-010A | MARINE BIOLOGICAL ASSOCIATION | NOT_COLLECTED | MID_BODY | SAMEA8724888 | SAMEA8724794 |
| wpSthLimi1 | MBA-201117-010A | MARINE BIOLOGICAL ASSOCIATION | NOT_COLLECTED | MID_BODY | SAMEA8724891 | SAMEA8724794 |
| wpSthLimi1 | MBA-201117-010A | MARINE BIOLOGICAL ASSOCIATION | NOT_COLLECTED | MID_BODY | SAMEA8724884 | SAMEA8724794 |
| wpSthLimi1 | MBA-201117-010A | MARINE BIOLOGICAL ASSOCIATION | NOT_COLLECTED | MID_BODY | SAMEA8724887 | SAMEA8724794 |
| wpSthLimi1 | MBA-201117-010A | MARINE BIOLOGICAL ASSOCIATION | NOT_COLLECTED | MID_BODY | SAMEA8724882 | SAMEA8724794 |
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 | wpSthLimi1 | 31 | 25.15 | 1,553,528,257 | 52.96 | 1.52 | 98.23 | 1.09 |   histogram.txt |
| pacbio | wpSthLimi1 | 31 | 22.71 | 951,013,735 | 35.03 | 1.57 | 97.46 | 0.32 |   histogram.txt |
| hic-arima2 | wpSthLimi1 | 31 | 102.1 | 1,022,526,727 | 34.10 | 2.20 | 96.49 | 0.44 |   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 | wpSthLimi1 | 2021-06-12 | 83253 | m64089e_210612_231801 | B01 | 1011 | 14,362,539,669 | 12,710 | SAMEA8724886 | ERR8978461 | |
| PacBio - HiFi | wpSthLimi1 | 2021-06-24 | 83718 | m64229e_210624_142755 | A01 | 1011 | 15,845,831,870 | 12,378 | SAMEA8724886 | ERR8978462 | |
| PacBio - HiFi | wpSthLimi1 | 2021-06-25 | 83718 | m64229e_210625_232523 | B01 | 1011 | 17,668,789,832 | 12,109 | SAMEA8724886 | ERR8978463 |
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 | wpSthLimi1 | 2021-06-28 | 38911_3#2 | 95,954,832 | 14,489,179,632 | SAMEA8724886 | qc complete | ||
| Chromium genome | wpSthLimi1 | 2021-06-28 | 38911_3#1 | 284,262,456 | 42,923,630,856 | SAMEA8724886 | qc complete | Sthenelais limicola (1.00) | |
| Chromium genome | wpSthLimi1 | 2021-06-28 | 38911_3#3 | 301,083,810 | 45,463,655,310 | SAMEA8724886 | qc complete | ||
| Chromium genome | wpSthLimi1 | 2021-06-28 | 38911_3#4 | 320,502,422 | 48,395,865,722 | SAMEA8724886 | qc complete | ||
| Hi-C - Arima v2 | wpSthLimi1 | 2021-10-05 | 41252_1#1 | 1,968,904,148 | 297,304,526,348 | SAMEA8724891 | ERR8702825 | qc complete | |
| RNA PolyA | wpSthLimi1 | 2022-08-23 | 45657_1#47 | 54,189,256 | 8,182,577,656 | SAMEA8724882 | ERR10123685 | qc complete | Sthenelais limicola (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 |
|---|---|
| 0.903965 | 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 |
|---|---|---|---|
| wpSthLimi1 | atg001058l | 1909 |
|
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 |
|---|---|
| wpSthLimi1 |    |
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
BTK datasets:
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| wpSthLimi1 | hifiasm.scaff_original.salsa | 2021-10-05 | 13,080,547 | 1,357 | 104,402,906 | 797 | 1,207,458,394 | - | |
| wpSthLimi1 | hifiasm.scaff_original.yahs | 2021-10-05 | 13,080,547 | 1,383 | 147,304,111 | 610 | 1,207,332,994 | - | |
| wpSthLimi1 | hifiasm.purging_e | 2021-10-05 | 9,176,718 | 1,544 | 14,621,522 | 1,331 | 1,174,590,164 | - | |
| wpSthLimi1 | hifiasm.purging_calcuts_36 | 2021-10-05 | 13,080,547 | 1,332 | 1,207,303,092 | - | |||
| wpSthLimi1 | hifiasm.purging_calcuts_27 | 2021-10-05 | 13,080,547 | 1,346 | 1,212,627,025 | - | |||
| wpSthLimi1 | hifiasm.purging | 2021-10-05 | 13,080,547 | 1,333 | 1,207,178,394 | C:95.8%[S:93.4%,D:2.4%],F:2.7%,M:1.5%,n:954 | Q51.0-C86.4(10X); Q62.2-C98.5(HiFi) | ||
| wpSthLimi1 | hifiasm.scaff.salsa | 2021-10-05 | 9,176,718 | 1,564 | 108,563,888 | 934 | 1,174,900,265 | - | |
| wpSthLimi1 | hifiasm.scaff.yahs | 2021-10-05 | 9,176,718 | 1,586 | 140,026,770 | 727 | 1,174,757,065 | - | |
| wpSthLimi1 | hifiasm | 2021-10-05 | 6,688,580 | 2,114 | 1,364,979,647 | C:95.8%[S:88.6%,D:7.2%],F:2.7%,M:1.5%,n:954 | Q49.7-C86.5(10X); Q61.4-C98.6(HiFi) | ||
| wpSthLimi1 | hifiasm.scaff_polished.salsa | 2021-10-05 | 13,080,409 | 1,356 | 116,803,760 | 809 | 1,207,423,400 | - | |
| wpSthLimi1 | hifiasm.scaff_polished.yahs | 2021-10-05 | 13,080,409 | 1,369 | 127,386,608 | 900 | 1,207,243,700 | - | |
| wpSthLimi1 | hicanu.purging | 2021-10-05 | 3,012,173 | 1,940 | 1,259,196,863 | C:95.5%[S:91.8%,D:3.7%],F:3.0%,M:1.5%,n:954 | Q51.3-C86.6(10X); Q67.7-C98.6(HiFi) | ||
| wpSthLimi1 | hicanu | 2021-10-05 | 2,241,422 | 6,813 | 2,328,976,344 | C:96.1%[S:4.8%,D:91.3%],F:2.5%,M:1.4%,n:954 | Q43.3-C86.6(10X); Q66.4-C98.7(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | reference |
|---|---|---|---|---|---|---|---|---|
| wpSthLimi1 | mitohifi.hifiasm | mito | 2021-10-05 | 17,436 | 33 | ND1 | NC_057074.1; 15,904 bp; 37 genes | |
| wpSthLimi1 | mitohifi.hicanu | mito | 2021-10-05 | 46,002 | 55 | None | NC_057074.1; 15,904 bp; 37 genes | |
| wpSthLimi1 | mitohifi.reads | mito | 2021-10-05 | 23,053 | 33 | None | NC_057074.1; 15,904 bp; 37 genes |
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