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).

Loading, please wait
tolid
specimen_id
gal
sex
organism_part
biosample
biospecimen
xbBatSept1URI0000005UNIVERSITY OF RHODE ISLANDNOT_COLLECTEDGILL_ANIMALSAMEA111532992SAMEA111532939
xbBatSept10URI0000014UNIVERSITY OF RHODE ISLANDNOT_COLLECTEDGILL_ANIMALSAMEA111533001SAMEA111532948
xbBatSept2URI0000006UNIVERSITY OF RHODE ISLANDNOT_COLLECTEDGILL_ANIMALSAMEA111532993SAMEA111532940
xbBatSept3URI0000007UNIVERSITY OF RHODE ISLANDNOT_COLLECTEDGILL_ANIMALSAMEA111532994SAMEA111532941
xbBatSept4URI0000008UNIVERSITY OF RHODE ISLANDNOT_COLLECTEDGILL_ANIMALSAMEA111532995SAMEA111532942
Showing 1 to 5 of 10 rows

Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

Loading, please wait
source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
illuminaxbBatSept13112.981,691,222,73261.870.8598.470.28
histogram.txt
hic-arima2xbBatSept13139.331,166,681,0880.00100.002.280.30
histogram.txt
pacbioxbBatSept23115.822,090,935,61069.520.9898.340.06
histogram.txt

Sequence data


PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

Loading, please wait
pipeline
specimen
date
run id
movie
well
tag
yield
N50
sample accession
run accession
barcode
PacBio - HiFixbBatSept22023-07-07TRACTION-RUN-670m84047_230707_113741_s4B01203467,714,006,1449,102SAMEA111532993ERR11809143
Showing 1 to 1 of 1 rows

ONT run data

Below are stats for each ONT seqeuncing run collected for this species.

Loading, please wait
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.

Loading, please wait
pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
StandardxbBatSept12023-07-3147686_2#15395,616,68859,738,119,888SAMEA111532992ERR11814111qc completeBathymodiolus septemdierum (1.00)
Hi-C - Arima v2xbBatSept12023-05-1547274_1#5833,063,032125,792,517,832SAMEA111532992ERR11814110qc completeBathymodiolus septemdierum (1.00)
RNA PolyAxbBatSept12023-11-2048093_1#1165,774,3509,931,926,850SAMEA111532992ERR12321230qc completeBathymodiolus septemdierum (1.00)
RNA PolyAxbBatSept22024-05-0948860_1#43157,915,21423,845,197,314SAMEA111532993qc complete
Showing 1 to 4 of 4 rows

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.

Loading, please wait
identity
info
0.923498NC_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 [...]
0.900394NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence
Showing 1 to 3 of 3 rows

Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

Loading, please wait
specimen
contig
SSU length
attributed taxonomy by SSU
xbBatSept2atg000624l983
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2atg002200l1030
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2atg003344l1813
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2ptg000011l1529
  • ENA: Bacteria;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Thioglobaceae;SUP05 cluster;
xbBatSept2ptg000019l831
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2ptg000201l1511
  • ENA: Bacteria;Proteobacteria;Epsilonproteobacteria;environmental samples;
  • SILVA: Bacteria;Campylobacterota;Campylobacteria;Campylobacterales;Helicobacteraceae;uncultured;
xbBatSept2ptg000508l993
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2ptg000639l1538
  • ENA: Bacteria;Chlamydiae;Parachlamydiales;
  • SILVA: Bacteria;Verrucomicrobiota;Chlamydiae;Chlamydiales;
xbBatSept2ptg001858l1818
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
xbBatSept2ptg003058l1810
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;Mytiloidea;Mytilidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Mollusca;Bivalvia;Pteriomorphia;Mytiloida;
Showing 1 to 10 of 11 rows rows per page

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.

Loading, please wait
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.

Loading, please wait
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.

Loading, please wait
specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
xbBatSept2hifiasm.purging2023-07-102,323,7631,4741,492,515,530C:87.2%[S:85.3%,D:1.9%],F:4.0%,M:8.8%,n:5295Q58.5-C96.6(HiFi)
xbBatSept2hifiasm2023-07-101,696,2614,0301,882,203,973C:87.5%[S:83.5%,D:4.0%],F:3.9%,M:8.6%,n:5295Q58.1-C97.5(HiFi)
xbBatSept2hifiasm.scaffolding.yahs2023-07-102,253,4831,57398,669,9135311,492,723,930C:88.1%[S:86.8%,D:1.3%],F:3.7%,M:8.2%,n:5295Q58.5-C96.6(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

Loading, please wait
specimen
asm
organelle
date
length
genes
frameshifts
is circular
seqs
reference
xbBatSept2mitohifi.hifiasmmito2023-07-1017,11137NoneTrue1NC_059708.1; 17,138 bp; 39 genes
xbBatSept2mitohifi.readsmito2023-07-1017,11136NoneTrue1NC_059708.1; 17,138 bp; 39 genes