Info

NCBI taxon id: 319673  NCBI; ENA; GoaT
Order: Akentrogonida
Family: Clistosaccidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Cirripedia;Rhizocephala;Clistosaccidae;Clistosaccus;
GoaT genome size (M): 1,841 (ancestor)
GoaT asm span (M): 264 (ancestor)
GoaT chr no.: 34 (ancestor)
GoaT haploid no.: 8 (ancestor)
GoaT ploidy: 6 (ancestor)
ToLID prefix: qxCliPagu

Specimens

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

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tolid
specimen_id
gal
sex
organism_part
biosample
biospecimen
qxCliPagu1SAN0000181SANGER INSTITUTEFEMALEGONADSAMEA7523196SAMEA7523100
qxCliPagu10SAN20000837SANGER INSTITUTEFEMALEWHOLE_ORGANISMSAMEA12813522SAMEA12813473
qxCliPagu11SAN20000842SANGER INSTITUTEFEMALEWHOLE_ORGANISMSAMEA12813528SAMEA12813478
qxCliPagu2SAN0000182SANGER INSTITUTEFEMALEGONADSAMEA7523197SAMEA7523101
qxCliPagu3SAN20000857SANGER INSTITUTEFEMALEWHOLE_ORGANISMSAMEA12813426SAMEA12813425
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Spectra estimates

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

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
pacbioqxCliPagu13136.345,048,42180.873.5587.493.25
histogram.txt
10xqxCliPagu13122.99727,619,42585.167.3882.961.14
histogram.txt
hic-arima2qxCliPagu23146.79723,602,41063.351.7196.160.62
histogram.txt
pacbioqxCliPagu931110950,645,25463.561.1991.660.30
histogram.txt
hic-arima2qxCliPagu93144.361,373,254,4990.00100.002.920.25
histogram.txt

Sequence data


PacBio run data

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

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pipeline
specimen
date
run id
movie
well
tag
yield
N50
sample accession
run accession
barcode
PacBio - HiFiqxCliPagu12020-10-2978010m64089_201029_104118A0110201,024,838,17811,222SAMEA7523196
PacBio - HiFiqxCliPagu92023-05-08TRACTION-RUN-574m64228e_230508_055021F01205422,872,403,19615,960SAMEA12813521
PacBio - HiFiqxCliPagu92024-02-23TRACTION-RUN-1140m84093_240223_154438_s4D01205418,538,781,06114,218SAMEA12813521
PacBio - HiFi (ULI)qxCliPagu92024-04-30TRACTION-RUN-1259m84098_240430_105248_s3B01200558,978,616,8788,385SAMEA12813521
PacBio - HiFiqxCliPagu92024-05-31TRACTION-RUN-1312m84047_240531_133150_s1A01207368,296,461,97715,522SAMEA12813521
PacBio - HiFiqxCliPagu92024-06-18TRACTION-RUN-1333m84098_240618_114443_s4D01205461,156,254,50511,742SAMEA12813521
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ONT run data

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

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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.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Chromium genomeqxCliPagu12020-10-2735278_8#5124,683,58018,827,220,580SAMEA7523196qc complete
Chromium genomeqxCliPagu12020-10-2735278_8#7101,487,53815,324,618,238SAMEA7523196qc complete
Chromium genomeqxCliPagu12020-10-2735278_8#8100,158,77615,123,975,176SAMEA7523196qc complete
Chromium genomeqxCliPagu12020-10-2735278_8#6109,847,21216,586,929,012SAMEA7523196qc complete
Hi-C - Arima v2qxCliPagu22020-11-1435430_3#4677,655,470102,325,975,970SAMEA7523197qc complete
Hi-C - Arima v2qxCliPagu92024-01-2648341_6-7#11,100,267,908166,140,454,108SAMEA12813521qc complete
RNA PolyAqxCliPagu62023-11-0248017_1#8557,197,1708,636,772,670SAMEA12813518qc complete
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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.

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identity
info
0.97809[2 seqs] NZ_FSRF01000002.1 Pseudoalteromonas sp. 13-15, whole genome shotgun sequence [...]
0.960395[2 seqs] NZ_LGBR01000001.1 Polaribacter dokdonensis DSW-5 contig1, whole genome shotgun sequence [...]
0.93735[2 seqs] NZ_CP012160.1 Octadecabacter temperatus strain SB1, complete genome [...]
0.934853[21 seqs] NZ_AULQ01000001.1 Mesoflavibacter zeaxanthinifaciens DSM 18436 H574DRAFT_scaffold00001.1_C, whole genome shotgun sequence [...]
0.934669[114 seqs] NZ_MKKN01000001.1 Vibrio sp. 10N.222.47.A9 10N.222.47.A9_contig_1, whole genome shotgun sequence [...]
0.934669[2 seqs] NC_011059.1 Prosthecochloris aestuarii DSM 271, complete genome [...]
0.933552[2 seqs] NZ_LGBR01000001.1 Polaribacter dokdonensis DSW-5 contig1, whole genome shotgun sequence [...]
0.932601[21 seqs] NZ_LOFG01000001.1 Pseudoalteromonas sp. H103 scaffold_1, whole genome shotgun sequence [...]
0.927097[2 seqs] NZ_CP012160.1 Octadecabacter temperatus strain SB1, complete genome [...]
0.925107[139 seqs] NZ_LNDJ01000001.1 Psychrobacter piscatorii strain LQ58 contig1, whole genome shotgun sequence [...]
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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

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specimen
contig
SSU length
attributed taxonomy by SSU
qxCliPagu9ptg000598c1522
  • ENA: Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;Winogradskyella;
qxCliPagu9ptg000632l660
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Hexanauplia;Cirripedia;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Crustacea;Maxillopoda;Thecostraca;
qxCliPagu9ptg000636l660
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Hexanauplia;Cirripedia;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Crustacea;Maxillopoda;Thecostraca;
qxCliPagu9ptg001014l1519
  • ENA: Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Tenacibaculum;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;
qxCliPagu9ptg001177l1518
  • ENA: Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;Flavobacteriaceae;Cellulophaga;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;Cellulophaga;
qxCliPagu9ptg001262l1767
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Hexanauplia;Cirripedia;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Crustacea;Maxillopoda;Thecostraca;
qxCliPagu9ptg001391l1521
  • ENA: Bacteria;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Crocinitomicaceae;Fluviicola;
qxCliPagu9ptg001642l1518
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;OCS116 cluster;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Chitinophagales;uncultured;
qxCliPagu9ptg002084l1523
  • ENA: Bacteria;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Chitinophagales;Saprospiraceae;Aureispira;
qxCliPagu9ptg002126l1460
  • ENA: Bacteria;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;Yoonia-Loktanella;
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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.

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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.

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specimen
visualisation
qxCliPagu1

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

  • qxCliPagu9.hifiasm.20240706

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
qxCliPagu9hifiasm.purging2024-07-061,921,4718,8471,589,249,356C:91.8%[S:80.8%,D:11.0%],F:3.7%,M:4.5%,n:1013Q50.9-C89.5(HiFi)
qxCliPagu9hifiasm.scaffolding.yahs2024-07-061,530,0009,38945,008,7557,7841,589,570,356C:92.1%[S:83.3%,D:8.8%],F:3.3%,M:4.6%,n:1013Q50.9-C89.5(HiFi)
qxCliPagu9hifiasm2024-07-061,345,10816,9434,252,308,217C:92.9%[S:2.8%,D:90.1%],F:3.1%,M:4.0%,n:1013Q52.7-C99.1(HiFi)
qxCliPagu9hifiasm-hic.purging2024-07-061,077,9899,6001,530,028,728C:91.3%[S:81.3%,D:10.0%],F:4.0%,M:4.7%,n:1013Q51.0-C87.5(HiFi)
qxCliPagu9hifiasm-hic.hap12024-07-06687,10823,2304,701,069,819C:93.0%[S:3.1%,D:89.9%],F:2.9%,M:4.1%,n:1013Q52.9-C99.1(HiFi)
qxCliPagu9hifiasm-hic.scaffolding_hap2.yahs2024-07-06515,41713,6213,218,415,383C:92.3%[S:5.3%,D:87.0%],F:3.4%,M:4.3%,n:1013Q54.4-C99.1(HiFi)
qxCliPagu9hifiasm-hic.hap22024-07-06674,7029,9573,218,415,383C:92.4%[S:5.0%,D:87.4%],F:3.4%,M:4.2%,n:1013Q54.4-C99.1(HiFi)
qxCliPagu9hifiasm-hic.purging2024-02-27994,8023,1051,024,817,115C:90.8%[S:83.1%,D:7.7%],F:3.9%,M:5.3%,n:1013Q53.4-C88.1(HiFi)
qxCliPagu9hifiasm-hic.hap12024-02-27400,71919,1342,672,009,808C:92.2%[S:12.3%,D:79.9%],F:3.4%,M:4.4%,n:1013Q51.4-C98.5(HiFi)
qxCliPagu9hifiasm-hic.scaffolding_hap2.yahs2024-02-27519,21010,758640,20410,3732,122,264,950C:91.2%[S:16.3%,D:74.9%],F:3.6%,M:5.2%,n:1013Q52.8-C98.5(HiFi)
qxCliPagu9hifiasm-hic.hap22024-02-27603,2428,8382,122,187,950C:91.2%[S:14.7%,D:76.5%],F:3.7%,M:5.1%,n:1013-
qxCliPagu9hifiasm.purging2024-02-271,675,3202,0551,029,249,894C:91.4%[S:84.0%,D:7.4%],F:3.7%,M:4.9%,n:1013Q53.7-C95.9(HiFi)
qxCliPagu9hifiasm.scaffolding.yahs2024-02-271,626,2962,27953,791,8701,2851,029,448,694C:91.6%[S:84.8%,D:6.8%],F:3.5%,M:4.9%,n:1013Q53.7-C95.9(HiFi)
qxCliPagu9hifiasm2024-02-27692,31714,7482,788,803,723C:92.3%[S:6.2%,D:86.1%],F:3.3%,M:4.4%,n:1013Q51.4-C98.6(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
seqs
reference
qxCliPagu9mitohifi.hifiasm-hicmito2024-02-2762,87330NoneTrue1MZ411548.1; 14,579 bp; 37 genes
qxCliPagu9mitohifi.hifiasmmito2024-02-2738,22930NoneTrue1MZ411548.1; 14,579 bp; 37 genes