Info

NCBI taxon id: 558755
Order: Cheilostomatida
Family: Cryptosulidae
NCBI lineage: Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Bryozoa;Gymnolaemata;Cheilostomatida;Flustrina;Schizoporelloidea;Cryptosulidae;Cryptosula;
GoaT genome size (M): 647 (ancestor)
GoaT asm span (M): 224 (ancestor)
GoaT chr no.: 5 (ancestor)
ToLID prefix: tzCryPall

Specimens

Below is information about specimens collected for this species retrieved from the Golden Record manifest.

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public_name
specimen_id
gal
sex
organism_part
biosample
biospecimen
tzCryPall1MBA-200715-002HMARINE BIOLOGICAL ASSOCIATIONHERMAPHRODITE_MONOECIOUSMODULAR_COLONYSAMEA7536671SAMEA7536575
tzCryPall2MBA-200715-002GMARINE BIOLOGICAL ASSOCIATIONHERMAPHRODITE_MONOECIOUSMODULAR_COLONYSAMEA7536672SAMEA7536576
tzCryPall3MBA-200715-002CMARINE BIOLOGICAL ASSOCIATIONHERMAPHRODITE_MONOECIOUSMODULAR_COLONYSAMEA7536673SAMEA7536577
tzCryPall4MBA-200715-002BMARINE BIOLOGICAL ASSOCIATIONHERMAPHRODITE_MONOECIOUSMODULAR_COLONYSAMEA7536674SAMEA7536578
tzCryPall5MBA-200715-002DMARINE BIOLOGICAL ASSOCIATIONHERMAPHRODITE_MONOECIOUSMODULAR_COLONYSAMEA7536676SAMEA7536579
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Spectra estimates

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

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
hic-arima2tzCryPall13170.61616,096,05568.644.8295.030.46
10xtzCryPall53124.881,090,119,81373.833.1196.540.85
pacbiotzCryPall53117.53567,211,21049.932.9296.410.38
hic-arima2tzCryPall53158.58657,452,39069.824.9994.590.67

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 - HiFitzCryPall52020-12-1879041m64089_201218_134712A01100122,412,142,79611,833SAMEA7536677ERR9863243
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Illumina run data

Illumina run stats.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Hi-C - Arima v2tzCryPall12021-03-2236943_2#2822,093,586124,136,131,486SAMEA7536671qc completeCryptosula pallasiana (0.99)
Chromium genometzCryPall52021-01-2936148_2#17169,711,48625,626,434,386SAMEA7536677qc complete
Chromium genometzCryPall52021-01-2936148_2#20145,735,36022,006,039,360SAMEA7536677qc completeCryptosula pallasiana (1.00)
Chromium genometzCryPall52021-01-2936148_2#18148,838,99222,474,687,792SAMEA7536677qc completeCryptosula pallasiana (1.00)
Chromium genometzCryPall52021-01-2936148_2#19178,842,82427,005,266,424SAMEA7536677qc completeCryptosula pallasiana (1.00)
Hi-C - Arima v2tzCryPall52021-02-1536276_1#5781,003,052117,931,460,852SAMEA7536676ERR9866429qc complete
RNA PolyAtzCryPall42021-08-0339723_6#1257,872,4788,738,744,178SAMEA7536674ERR9866430qc completeCryptosula pallasiana (1.00)
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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
0.955918[436 seqs] NZ_MKCO01000001.1 Epsilonproteobacteria bacterium LFT 1.7 Contig1, whole genome shotgun sequence [...]
0.953635[162 seqs] NZ_MAKF01000001.1 Vibrio splendidus strain 13B01 13B01_contig_0, whole genome shotgun sequence [...]
0.941819[13 seqs] NZ_CH672437.1 Marinomonas sp. MED121 scf_1099517007716 genomic scaffold, whole genome shotgun sequence [...]
0.937001[29 seqs] NZ_LODK01000001.1 Pseudoalteromonas sp. H100 scaffold_0.1, whole genome shotgun sequence [...]
0.926443NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.909369[69 seqs] NZ_JSEO01000001.1 Marinomonas sp. SBI8L contig_1, whole genome shotgun sequence [...]
0.906747[313 seqs] NZ_AJYW02000001.1 Vibrio genomosp. F6 str. FF-238 FF-238_contig_0, whole genome shotgun sequence [...]
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Species composition by small subunit (SSU) presence in the assembly.

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specimen
contig
SSU length
attributed taxonomy by SSU
tzCryPall5atg001691l1536
  • ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Colwelliaceae;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Colwelliaceae;
tzCryPall5ptg000234l1518
  • ENA: Bacteria;Bacteroidetes;Flavobacteriia;Flavobacteriales;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;Winogradskyella;
tzCryPall5ptg001370l1546
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Bryozoa;Gymnolaemata;Cheilostomatida;Flustrina;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Bryozoa;Gymnolaemata;Cheilostomatida;
tzCryPall5ptg001506l1535
  • ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Colwelliaceae;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Colwelliaceae;
tzCryPall5ptg002245l1458
  • ENA: Bacteria;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rhodobacterales;Rhodobacteraceae;
tzCryPall5ptg002410l1545
  • ENA: Unclassified;
  • SILVA: Unclassified;
tzCryPall5ptg002738l1845
  • ENA: Eukaryota;Metazoa;Lophotrochozoa;Bryozoa;Gymnolaemata;Cheilostomatida;Flustrina;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Lophotrochozoa;Bryozoa;Gymnolaemata;Cheilostomatida;
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Re-assembly of reads classified under each identified SSU Marker family.

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specimen
family
classified reads
original assembly
re-assembly
count
(%)
BUSCO
BUSCO
contigs
contig length
reads
BUSCO
contigs
contig length
additional reads
circos
tzCryPall5Colwelliaceae7,1680.34C:99.6%[S:2.9%,D:96.7%],F:0.4%,M:0.0%,n:820C:16.0%[S:16.0%,D:0.0%],F:1.7%,M:82.3%,n:820300.69Mb270C:43.7%[S:36.7%,D:7.0%],F:5.2%,M:51.1%,n:820692.58Mb347
tzCryPall5Flavobacteriaceae6,2790.3C:100.0%[S:0.4%,D:99.6%],F:0.0%,M:0.0%,n:733C:98.8%[S:81.7%,D:17.1%],F:0.7%,M:0.5%,n:733224.40Mb2,499C:99.2%[S:63.2%,D:36.0%],F:0.7%,M:0.1%,n:733485.64Mb203
tzCryPall5Rhodobacteraceae7,2300.35C:99.8%[S:3.6%,D:96.2%],F:0.2%,M:0.0%,n:833C:32.7%[S:29.7%,D:3.0%],F:3.8%,M:63.5%,n:833461.39Mb698-0.00Mb
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Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.

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specimen
visualisation
tzCryPall5

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

  • tzCryPall5.hifiasm.20220519

BTK datasets:


Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
tzCryPall5hifiasm.purging_e_352021-03-011,660,2662,493786,492,933-
tzCryPall5hifiasm.purging2021-03-011,660,2662,496787,479,135-
tzCryPall5hifiasm.purging_e2022-05-191,829,9072,0232,031,2941,747686,732,209C:83.9%[S:80.5%,D:3.4%],F:8.3%,M:7.8%,n:954-
tzCryPall5hifiasm.purging2022-05-192,017,1011,747736,264,438C:83.8%[S:76.9%,D:6.9%],F:8.3%,M:7.9%,n:954Q41.6-C85.3(10X); Q57.6-C97.7(HiFi)
tzCryPall5hifiasm.scaff.salsa2022-05-191,577,5452,06918,471,2271,249687,119,629-
tzCryPall5hifiasm.scaff.yahs2022-05-191,560,8932,14944,578,6951,279686,883,629Q49.0-C97.6(HiFi)
tzCryPall5hifiasm.scaff_purged_e.salsa2022-05-191,577,5632,07118,527,0551,264687,129,361-
tzCryPall5hifiasm.scaff_purged_e.yahs2022-05-191,557,0002,15243,304,7341,286686,899,061C:83.9%[S:80.5%,D:3.4%],F:8.1%,M:8.0%,n:954Q57.4-C97.6(HiFi)
tzCryPall5hifiasm.polishing2022-05-192,017,0761,747736,247,526C:83.8%[S:76.7%,D:7.1%],F:8.3%,M:7.9%,n:954Q42.9-C85.4(10X); Q49.3-C97.7(HiFi)
tzCryPall5hifiasm2022-05-191,528,6123,214952,483,818C:84.0%[S:62.9%,D:21.1%],F:8.1%,M:7.9%,n:954Q41.2-C86.2(10X); Q56.7-C98.6(HiFi)
tzCryPall5hifiasm.scaffolding.salsa2022-05-191,713,0231,82527,175,6051,067736,626,526C:83.9%[S:77.3%,D:6.6%],F:8.3%,M:7.8%,n:954Q42.9-C85.4(10X); Q49.3-C97.7(HiFi)
tzCryPall5hifiasm.scaffolding.yahs2022-05-191,726,0001,92146,744,4921,081736,415,526C:83.9%[S:77.4%,D:6.5%],F:8.1%,M:8.0%,n:954Q42.9-C85.4(10X); Q49.3-C97.7(HiFi)
tzCryPall5hicanu2021-09-05747,5359,3271,343,819,818C:84.3%[S:8.3%,D:76.0%],F:8.2%,M:7.5%,n:954Q40.3-C85.4(10X); Q66.5-C98.9(HiFi)
tzCryPall5hicanu.purging2021-09-051,021,3483,156774,227,578C:83.5%[S:76.5%,D:7.0%],F:8.6%,M:7.9%,n:954Q42.0-C85.0(10X); Q66.9-C98.3(HiFi)
tzCryPall5hifiasm.purging_e_352020-12-221,253,6052,6421,417,6252,316704,069,747-
tzCryPall5hifiasm.purging_e2020-12-221,256,3932,6481,417,6252,322704,738,926-
tzCryPall5hifiasm.purging_e_402020-12-221,253,6052,6401,417,6252,314704,280,650-
tzCryPall5hifiasm.purging2020-12-221,429,4882,322769,047,043-
tzCryPall5hifiasm.purging_352020-12-221,429,4882,317768,244,172-
tzCryPall5hifiasm2020-12-221,097,2934,8861,267,088,528-
tzCryPall5hifiasm.purging_222020-12-221,429,4882,332769,322,292-
tzCryPall5hifiasm.purging_402020-12-221,429,4882,315768,232,135-
tzCryPall5hicanu2020-12-22747,5359,3271,343,819,818-
tzCryPall5hicanu.purging_e2020-12-22914,6873,4471,008,2593,156723,858,402-
tzCryPall5hicanu.purging2020-12-221,021,3483,155774,179,900-
tzCryPall5hicanu.purging_352020-12-221,021,3483,145773,785,269-
tzCryPall5hicanu.purging_222020-12-221,021,3483,165774,725,021-
tzCryPall5hicanu.purging_402020-12-221,021,3483,144773,761,405-
tzCryPall5hifiasm.purging_e_2021-04-201,044,4402,5391,094,1712,435582,392,887-
tzCryPall5hifiasm.purging_e2021-04-201,044,4402,5391,094,1712,435582,392,887-
tzCryPall5hifiasm.purging2021-04-201,094,1712,437595,593,583-
tzCryPall5hifiasm.purging_2021-04-201,094,1712,437595,593,583-
tzCryPall5hifiasm.purging_e2021-05-121,971,3761,9882,116,2481,752665,945,102-
tzCryPall5hifiasm.purging2021-05-122,090,4781,752701,483,876-
tzCryPall5hifiasm.purging2021-04-262,106,9481,761702,524,924-
tzCryPall5hifiasm-hic2022-05-191,489,0813,275957,703,189C:83.8%[S:62.6%,D:21.2%],F:8.2%,M:8.0%,n:954Q41.2-C86.2(10X); Q56.9-C98.7(HiFi)
tzCryPall5hifiasm.purging2022-01-252,079,7991,722725,915,888C:66.6%[S:58.1%,D:8.5%],F:10.8%,M:22.6%,n:1367-
tzCryPall5hifiasm.purging2021-09-052,060,4871,760701,097,205C:82.9%[S:77.0%,D:5.9%],F:8.3%,M:8.8%,n:954Q41.5-C84.7(10X); Q57.9-C98.0(HiFi)
tzCryPall5hifiasm2021-09-051,557,5373,398929,673,972C:83.8%[S:67.0%,D:16.8%],F:8.3%,M:7.9%,n:954Q41.3-C85.4(10X); Q56.8-C98.8(HiFi)
tzCryPall5hicanu2022-05-19700,2728,9791,318,162,552C:84.3%[S:8.7%,D:75.6%],F:8.3%,M:7.4%,n:954Q40.3-C99.4(10X); Q64.1-C100.0(HiFi)
tzCryPall5hicanu.purging2022-05-19917,3393,252766,886,065C:83.6%[S:76.6%,D:7.0%],F:8.3%,M:8.1%,n:954Q41.5-C85.5(10X); Q64.4-C97.9(HiFi)
tzCryPall5hifiasm.purging_hap12022-01-241,212,1421,700567,553,323C:65.0%[S:62.3%,D:2.7%],F:10.1%,M:24.9%,n:1367-
tzCryPall5hifiasm.purging_hap22022-01-241,252,0142,041604,059,316C:65.9%[S:62.2%,D:3.7%],F:11.3%,M:22.8%,n:1367-
tzCryPall5hifiasm.purging_e2021-04-011,201,9822,8771,328,7012,561709,800,872-
tzCryPall5hifiasm.purging2021-04-011,381,1632,563774,477,152-

Organelles

In-progress organelle results from MitoHiFi2.

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specimen
asm
date
length
genes
frameshifts
is circular
reference
No matching records found