Bathymodiolus septemdierum
NOT_APPLICABLE
Info
| NCBI taxon id: | 220392 NCBI; ENA; GoaT |
|---|---|
| Order: | Mytiloida |
| Family: | Mytilidae |
| NCBI lineage: | Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Bivalvia;Autobranchia;Pteriomorphia;Mytilida;Mytiloidea;Mytilidae;Bathymodiolinae;Bathymodiolus; |
| GoaT genome size (M): | 1,452 (ancestor) |
| GoaT asm span (M): | 1,428 (direct) |
| GoaT chr no.: | 38 (ancestor) |
| GoaT haploid no.: | 14 (ancestor) |
| GoaT ploidy: | 2 (ancestor) |
| ToLID prefix: | xbBatSept |
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 |
|---|---|---|---|---|---|---|
| xbBatSept1 | URI0000005 | UNIVERSITY OF RHODE ISLAND | NOT_COLLECTED | GILL_ANIMAL | SAMEA111532992 | SAMEA111532939 |
| xbBatSept10 | URI0000014 | UNIVERSITY OF RHODE ISLAND | NOT_COLLECTED | GILL_ANIMAL | SAMEA111533001 | SAMEA111532948 |
| xbBatSept2 | URI0000006 | UNIVERSITY OF RHODE ISLAND | NOT_COLLECTED | GILL_ANIMAL | SAMEA111532993 | SAMEA111532940 |
| xbBatSept3 | URI0000007 | UNIVERSITY OF RHODE ISLAND | NOT_COLLECTED | GILL_ANIMAL | SAMEA111532994 | SAMEA111532941 |
| xbBatSept4 | URI0000008 | UNIVERSITY OF RHODE ISLAND | NOT_COLLECTED | GILL_ANIMAL | SAMEA111532995 | SAMEA111532942 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| illumina | xbBatSept1 | 31 | 12.98 | 1,691,222,732 | 61.87 | 0.85 | 98.47 | 0.28 |   histogram.txt |
| hic-arima2 | xbBatSept1 | 31 | 39.33 | 1,166,681,088 | 0.00 | 100.00 | 2.28 | 0.30 |   histogram.txt |
| pacbio | xbBatSept2 | 31 | 15.82 | 2,090,935,610 | 69.52 | 0.98 | 98.34 | 0.06 |   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 | xbBatSept2 | 2023-07-07 | TRACTION-RUN-670 | m84047_230707_113741_s4 | B01 | 2034 | 67,714,006,144 | 9,102 | SAMEA111532993 | ERR11809143 |
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 |
|---|---|---|---|---|---|---|---|---|---|
| Standard | xbBatSept1 | 2023-07-31 | 47686_2#15 | 395,616,688 | 59,738,119,888 | SAMEA111532992 | ERR11814111 | qc complete | Bathymodiolus septemdierum (1.00) |
| Hi-C - Arima v2 | xbBatSept1 | 2023-05-15 | 47274_1#5 | 833,063,032 | 125,792,517,832 | SAMEA111532992 | ERR11814110 | qc complete | Bathymodiolus septemdierum (1.00) |
| RNA PolyA | xbBatSept1 | 2023-11-20 | 48093_1#11 | 65,774,350 | 9,931,926,850 | SAMEA111532992 | ERR12321230 | qc complete | Bathymodiolus septemdierum (1.00) |
| RNA PolyA | xbBatSept2 | 2024-05-09 | 48860_1#43 | 157,915,214 | 23,845,197,314 | SAMEA111532993 | qc complete |
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 |
|---|---|
| 0.923498 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.902135 | [2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...] |
| 0.900394 | NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| xbBatSept2 | atg000624l | 983 |
|
| xbBatSept2 | atg002200l | 1030 |
|
| xbBatSept2 | atg003344l | 1813 |
|
| xbBatSept2 | ptg000011l | 1529 |
|
| xbBatSept2 | ptg000019l | 831 |
|
| xbBatSept2 | ptg000201l | 1511 |
|
| xbBatSept2 | ptg000508l | 993 |
|
| xbBatSept2 | ptg000639l | 1538 |
|
| xbBatSept2 | ptg001858l | 1818 |
|
| xbBatSept2 | ptg003058l | 1810 |
|
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 |
|---|---|
| No matching records found | |
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
xbBatSept2.hifiasm.20230710
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| xbBatSept2 | hifiasm.purging | 2023-07-10 | 2,323,763 | 1,474 | 1,492,515,530 | C:87.2%[S:85.3%,D:1.9%],F:4.0%,M:8.8%,n:5295 | Q58.5-C96.6(HiFi) | ||
| xbBatSept2 | hifiasm | 2023-07-10 | 1,696,261 | 4,030 | 1,882,203,973 | C:87.5%[S:83.5%,D:4.0%],F:3.9%,M:8.6%,n:5295 | Q58.1-C97.5(HiFi) | ||
| xbBatSept2 | hifiasm.scaffolding.yahs | 2023-07-10 | 2,253,483 | 1,573 | 98,669,913 | 531 | 1,492,723,930 | C:88.1%[S:86.8%,D:1.3%],F:3.7%,M:8.2%,n:5295 | Q58.5-C96.6(HiFi) |
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| xbBatSept2 | mitohifi.hifiasm | mito | 2023-07-10 | 17,111 | 37 | None | True | 1 | NC_059708.1; 17,138 bp; 39 genes |
| xbBatSept2 | mitohifi.reads | mito | 2023-07-10 | 17,111 | 36 | None | True | 1 | NC_059708.1; 17,138 bp; 39 genes |
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