Info

NCBI taxon id: 2813772  NCBI; ENA; GoaT
Order: Suessiales
Family: Symbiodiniaceae
NCBI lineage: Eukaryota;Sar;Alveolata;Dinophyceae;Suessiales;Symbiodiniaceae;Gerakladium;
GoaT genome size (M): 115 (ancestor)
GoaT asm span (M): 937 (ancestor)
GoaT chr no.: 24 (ancestor)
GoaT haploid no.: 5 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: pyGerJepo

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
pyGerJepo1UDUK0000095UNIVERSITY OF DERBYNOT_APPLICABLEWHOLE_ORGANISMSAMEA8579652SAMEA8579611
pyGerJepo4UDUK0000098UNIVERSITY OF DERBYNOT_APPLICABLEWHOLE_ORGANISMSAMEA8579655SAMEA8579614
Showing 1 to 2 of 2 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
pacbiopyGerJepo431103203,208,3840.0038.591.770.04
histogram.txt
pacbiopyGerJepo13127.761,448,447,63956.390.2595.780.10
histogram.txt
hic-arima2pyGerJepo13123.51,724,658,7020.00100.006.730.18
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 - HiFi (ULI)pyGerJepo12022-04-08TRACTION-RUN-87m64229e_220408_002506B01-23,327,646,6439,347SAMEA8579652ERR12666671
PacBio - HiFi (ULI)pyGerJepo12024-01-05TRACTION-RUN-1042m84093_240105_155132_s3A01-59,838,537,6849,266SAMEA8579652pending
PacBio - HiFi (ULI)pyGerJepo42024-02-27TRACTION-RUN-1146m84093_240227_112544_s1A01204242,536,768,12710,339SAMEA8579655
Showing 1 to 3 of 3 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
Hi-C - Arima v2pyGerJepo12021-09-1340749_1#7708,146,344106,930,097,944SAMEA8579652ERR12654651qc complete
Showing 1 to 1 of 1 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
0.992513NC_013222.1 Robiginitalea biformata HTCC2501, complete genome
0.987996[124 seqs] NZ_ACNO01000124.1 Rhodococcus erythropolis SK121 contig00004, whole genome shotgun sequence [...]
0.987263[62 seqs] NZ_FNYY01000061.1 Marinovum algicola strain FF3, whole genome shotgun sequence [...]
0.984932[378 seqs] NZ_LWEI01000001.1 Alcanivorax sp. HI0003 HI0003_c1, whole genome shotgun sequence [...]
0.984738[181 seqs] NZ_JXMT01000001.1 Labrenzia aggregata strain LZB033 contig1, whole genome shotgun sequence [...]
0.98125[38 seqs] NZ_LXYO01000001.1 Marinobacter sp. EhC06 A7_Contig1, whole genome shotgun sequence [...]
0.968895[21 seqs] NZ_LXRF01000001.1 Marinobacter adhaerens strain PBVC038 contig_0, whole genome shotgun sequence [...]
0.956847[47 seqs] NZ_MAYB01000010.1 Nitratireductor aquibiodomus strain EBB 35.1 NODE_10_length_108672_cov_46.7571_ID_2876, whole genome shotgun sequence [...]
0.948163[5 seqs] NZ_LNUS01000004.1 Staphylococcus epidermidis strain AU23 map unlocalized plasmid unnamed contig_5, whole genome shotgun sequence [...]
0.942602[44 seqs] NZ_LMFB01000001.1 Rhizobium sp. Root483D2 contig_1, whole genome shotgun sequence [...]
Showing 1 to 10 of 26 rows rows per page

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

Loading, please wait
specimen
contig
SSU length
attributed taxonomy by SSU
pyGerJepo4atg000789l1521
  • ENA: Bacteria;
  • SILVA: Bacteria;Actinobacteriota;Actinobacteria;Micrococcales;Microbacteriaceae;
pyGerJepo1atg001550l1800
  • ENA: Eukaryota;Alveolata;Dinophyceae;Suessiales;Symbiodiniaceae;Symbiodinium;
  • SILVA: Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Suessiaceae;Symbiodinium;
pyGerJepo4atg002274l1798
  • ENA: Eukaryota;Alveolata;Dinophyceae;Suessiales;Symbiodiniaceae;Symbiodinium;
  • SILVA: Eukaryota;SAR;Alveolata;Dinoflagellata;Dinophyceae;Gymnodiniphycidae;Suessiaceae;Symbiodinium;
pyGerJepo1atg004312l924
  • ENA: Unclassified;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;
pyGerJepo4ptg000002l1520
  • ENA: Bacteria;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Flavobacteriales;Flavobacteriaceae;
pyGerJepo4ptg000003l1532
  • ENA: Unclassified;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudohongiellaceae;Pseudohongiella;
pyGerJepo4ptg000004l1517
  • ENA: Bacteria;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;uncultured;
pyGerJepo4ptg000006c1521
  • ENA: Bacteria;environmental samples;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;uncultured;
pyGerJepo4ptg000007c1515
  • ENA: unclassified sequences;environmental samples;
  • SILVA: Bacteria;Bacteroidota;Bacteroidia;Cytophagales;Cyclobacteriaceae;Marinoscillum;
pyGerJepo4ptg000008c1492
  • ENA: Bacteria;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Terasakiellaceae;uncultured;
Showing 1 to 10 of 108 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
pyGerJepo1Alcanivoracaceae6,7150.25-C:2.4%[S:2.4%,D:0.0%],F:0.8%,M:96.8%,n:12410.02Mb20C:99.7%[S:10.8%,D:88.9%],F:0.0%,M:0.3%,n:6196212.98Mb5,010
pyGerJepo1Balneolaceae84,9883.15Too many reads - NA C:97.6%[S:11.3%,D:86.3%],F:1.6%,M:0.8%,n:1241017.25Mb62,639-0.00Mb
pyGerJepo1Cyclobacteriaceae55,0592.04Too many reads - NA C:60.8%[S:30.9%,D:29.9%],F:0.9%,M:38.3%,n:7681693.30Mb5,411-0.00Mb
pyGerJepo1Flavobacteriaceae65,4782.43Too many reads - NA C:90.5%[S:57.8%,D:32.7%],F:1.4%,M:8.1%,n:7331226.43Mb12,794-0.00Mb
pyGerJepo1Halieaceae23,2950.86C:99.9%[S:0.2%,D:99.7%],F:0.0%,M:0.1%,n:913C:99.2%[S:96.1%,D:3.1%],F:0.2%,M:0.6%,n:91374.23Mb19,061C:100.0%[S:4.8%,D:95.2%],F:0.0%,M:0.0%,n:1243811.09Mb2,043
pyGerJepo1Hyphomonadaceae4,0400.15C:98.7%[S:1.2%,D:97.5%],F:0.7%,M:0.6%,n:432C:0.7%[S:0.7%,D:0.0%],F:0.2%,M:99.1%,n:43230.04Mb23C:98.1%[S:85.6%,D:12.5%],F:0.2%,M:1.7%,n:432244.15Mb2,691
pyGerJepo1Marinobacteraceae26,8841C:100.0%[S:0.0%,D:100.0%],F:0.0%,M:0.0%,n:124C:92.3%[S:69.8%,D:22.5%],F:1.4%,M:6.3%,n:782205.04Mb11,352C:98.8%[S:6.6%,D:92.2%],F:0.1%,M:1.1%,n:78217924.42Mb10,414
pyGerJepo1Parvibaculaceae32,1591.19C:100.0%[S:0.2%,D:99.8%],F:0.0%,M:0.0%,n:432C:100.0%[S:98.4%,D:1.6%],F:0.0%,M:0.0%,n:43283.74Mb29,374C:66.9%[S:50.8%,D:16.1%],F:0.8%,M:32.3%,n:124792.89Mb271
pyGerJepo1Piscirickettsiaceae4,1730.15C:99.4%[S:1.4%,D:98.0%],F:0.0%,M:0.6%,n:491C:47.7%[S:47.7%,D:0.0%],F:1.8%,M:50.5%,n:491451.17Mb988C:98.8%[S:31.6%,D:67.2%],F:0.0%,M:1.2%,n:491565.52Mb1,578
pyGerJepo1Reichenbachiellaceae45,7421.7Too many reads - NA C:95.5%[S:53.6%,D:41.9%],F:0.0%,M:4.5%,n:768796.01Mb29,835-0.00Mb
Showing 1 to 10 of 16 rows rows per page

Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.

Loading, please wait
specimen
visualisation
pyGerJepo1

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

  • pyGerJepo4.hifiasm.20240301
  • pyGerJepo1.hifiasm.20240109

Assemblies

In-progress assembly QC.

Loading, please wait
specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
pyGerJepo1hifiasm2022-06-09145,79710,527900,342,416C:54.4%[S:38.0%,D:16.4%],F:11.7%,M:33.9%,n:171Q51.4-C94.2(HiFi)
pyGerJepo1hifiasm2024-03-08942,8874,4931,219,720,069C:70.2%[S:50.9%,D:19.3%],F:12.9%,M:16.9%,n:171Q52.2-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08744,2052,850943,2402,2531,047,988,838Q52.3-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08949,6592,2531,072,731,441Q52.3-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08741,0583,299929,5422,7201,074,427,239Q52.2-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08744,2052,899942,7652,3071,052,276,685Q52.3-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08948,0632,3071,076,963,740Q52.3-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-03-08937,2732,7201,094,344,224Q52.2-C99.6(HiFi)
pyGerJepo1hifiasm.scaffolding.yahs2024-03-08731,3292,940920,5422,3481,052,276,685-
pyGerJepo1hicanu.purging2022-08-19284,6248,6091,116,047,981C:67.8%[S:49.7%,D:18.1%],F:13.5%,M:18.7%,n:171Q56.6-C95.5(HiFi)
pyGerJepo1hicanu2022-08-19263,89415,2561,257,742,003C:67.8%[S:49.1%,D:18.7%],F:13.5%,M:18.7%,n:171Q56.9-C100.0(HiFi)
pyGerJepo4hifiasm.purging2024-03-01542,5142,279470,725,775C:63.8%[S:46.8%,D:17.0%],F:8.2%,M:28.0%,n:171Q56.5-C99.7(HiFi)
pyGerJepo4hifiasm2024-03-01368,1344,405535,987,441C:64.4%[S:47.4%,D:17.0%],F:8.2%,M:27.4%,n:171Q55.7-C99.7(HiFi)
pyGerJepo4hifiasm.scaffolding.yahs2024-03-01409,8443,374502,4513,301470,740,375C:61.9%[S:44.4%,D:17.5%],F:9.4%,M:28.7%,n:171Q56.5-C99.7(HiFi)
pyGerJepo1hifiasm-hic.hap12024-01-09744,5595,7421,236,330,698C:69.0%[S:49.7%,D:19.3%],F:14.0%,M:17.0%,n:171Q52.0-C99.6(HiFi)
pyGerJepo1hifiasm-hic.purging2024-01-09767,8743,8341,146,152,286C:69.0%[S:50.3%,D:18.7%],F:14.0%,M:17.0%,n:171Q52.2-C96.6(HiFi)
pyGerJepo1hifiasm-hic.hap22024-01-09819,3392,7551,143,534,059C:68.4%[S:49.7%,D:18.7%],F:13.5%,M:18.1%,n:171-
pyGerJepo1hifiasm-hic.scaffolding.yahs2024-01-09751,6603,8971,146,152,286C:69.0%[S:50.3%,D:18.7%],F:14.0%,M:17.0%,n:171Q52.2-C96.6(HiFi)
pyGerJepo1hifiasm2022-08-19461,9085,1511,029,541,669C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171Q53.3-C99.1(HiFi)
pyGerJepo1hifiasm.purging2022-08-19455,7834,451979,024,739C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171Q53.2-C95.3(HiFi)
pyGerJepo1hifiasm.scaffolding.salsa2022-08-19453,9994,455456,9444,437979,033,739C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171Q53.2-C95.3(HiFi)
pyGerJepo1hifiasm.scaffolding.yahs2022-08-19447,5284,495979,024,739C:63.1%[S:45.0%,D:18.1%],F:12.9%,M:24.0%,n:171Q53.2-C95.3(HiFi)
pyGerJepo1hicanu2022-06-0974,39622,8951,107,005,521C:63.2%[S:46.8%,D:16.4%],F:11.7%,M:25.1%,n:171Q56.8-C100.0(HiFi)
pyGerJepo1hifiasm.purging.202401152024-01-09852,6953,1101,120,628,368Q52.3-C96.7(HiFi)
pyGerJepo1hifiasm.scaffolding.20240115.yahs2024-01-09833,3583,1541,120,628,368-
pyGerJepo1hifiasm.scaffolding.20240115.yahs2024-01-09797,2502,2801,000,599,496-
pyGerJepo1hifiasm.scaffolding.20240115.yahs2024-01-0934,71349314,185,139-
pyGerJepo1hifiasm.scaffolding.20240115.yahs2024-01-09833,3583,1541,120,628,368-
pyGerJepo1hifiasm2024-01-09851,3715,3321,263,059,888C:69.6%[S:50.3%,D:19.3%],F:13.5%,M:16.9%,n:171Q52.3-C99.6(HiFi)
pyGerJepo1hifiasm.purging2024-01-09855,5273,6031,185,640,929C:69.6%[S:50.9%,D:18.7%],F:13.5%,M:16.9%,n:171Q52.3-C97.5(HiFi)
pyGerJepo1hifiasm.scaffolding.yahs2024-01-09836,6803,6681,185,640,929C:69.6%[S:50.9%,D:18.7%],F:13.5%,M:16.9%,n:171Q52.3-C97.5(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

Loading, please wait
specimen
asm
organelle
date
length
genes
frameshifts
is circular
seqs
reference
pyGerJepo1mitohifi.hifiasm-hicmito2022-08-1947,3632NoneFalse1NC_064340.1; 47,310 bp; 59 genes
pyGerJepo1mitohifi.hicanumito2022-08-1917,4288NoneFalse1NC_064340.1; 47,310 bp; 59 genes
pyGerJepo1mitohifi.readspltd2022-08-1933,0936NoneFalse1LC716140.1; 100,773 bp; 28 genes
pyGerJepo1mitohifi.readsmito2022-08-1913,2695NoneFalse1NC_064340.1; 47,310 bp; 59 genes
pyGerJepo4mitohifi.hifiasmmito2024-03-0123,52915NoneFalse1NC_058286.1; 25,726 bp; 29 genes
pyGerJepo1mitohifi.hifiasm-hicmito2024-01-0954,9785NoneFalse1MT941069.1; 41,256 bp; 47 genes
pyGerJepo1mitohifi.hifiasmmito2022-08-1947,3632NoneFalse1NC_064340.1; 47,310 bp; 59 genes
pyGerJepo1mitohifi.readsmito2022-06-0921,2683NoneFalse1NC_058286.1; 25,726 bp; 29 genes
pyGerJepo1mitohifi.hifiasmmito2024-01-0916,0609NoneFalse1MT941069.1; 41,256 bp; 47 genes