Tree of Life QC

Info

NCBI taxon id: 2721265  NCBI; ENA; GoaT
Order: Araneae
Family: Dysderidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;Araneomorphae;Haplogynae;Dysderoidea;Dysderidae;Parastalita;
GoaT genome size (M): 2,934 (ancestor)
GoaT asm span (M): 1,365 (ancestor)
GoaT chr no.: 21 (ancestor)
GoaT haploid no.: 11 (ancestor)
GoaT ploidy: 6 (ancestor)
ToLID prefix: qqParStyg

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
qqParStyg1ERGA_MP_HR_02SANGER INSTITUTEMALELEGSAMEA14515633SAMEA14515603
qqParStyg1ERGA_MP_HR_02SANGER INSTITUTEMALELEGSAMEA14515632SAMEA14515603
qqParStyg1ERGA_MP_HR_02SANGER INSTITUTEMALECEPHALOTHORAXSAMEA14515634SAMEA14515603
qqParStyg2SAN0001792SANGER INSTITUTEFEMALEWHOLE_ORGANISMSAMEA10458246SAMEA10458234
qqParStyg3SAN0001793SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA10458247SAMEA10458235
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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
pacbioqqParStyg23129.29239,614,88523.4212.3294.490.21
hic-arima2qqParStyg63137.574,293,098,194100.873.4886.140.27
hic-arima2qqParStyg131168.11,160,217,54149.532.2697.730.27
hic-arima2qqParStyg33190.16607,063,09169.492.3094.650.32

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 - HiFi (ULI)qqParStyg22022-04-10TRACTION-RUN-91m64230e_220410_202139D01-15,677,813,5616,279SAMEA10458246
PacBio - HiFiqqParStyg22022-10-01TRACTION-RUN-274m64230e_221001_191238C0110124,724,899,89510,016SAMEA10458246
PacBio - HiFi (ULI)qqParStyg22023-01-20TRACTION-RUN-421m64016e_230120_145448A01-17,268,746,9456,767SAMEA10458246
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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 v2qqParStyg62023-08-2147768_1#22,901,433,974438,116,530,074SAMEA14515643qc complete
Hi-C - Arima v2qqParStyg12023-09-1147798_4#23,507,736,924529,668,275,524SAMEA14515634qc complete
Hi-C - Arima v2qqParStyg32022-02-0943500_3#6998,577,702150,785,233,002SAMEA10458247qc completeParastalita stygia (1.00)
RNA PolyAqqParStyg42023-06-1947488_1#9071,433,49610,786,457,896SAMEA14515637qc completeParastalita stygia (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
0.937523NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.910933NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.908727[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.907083[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.906067[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.904677[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.904677NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.903605NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.901[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.901[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, 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
qqParStyg2ptg002612l1811
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;
qqParStyg2ptg017750l605
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Araneae;
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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
qqParStyg2

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

  • qqParStyg2.hifiasm.20240127

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
qqParStyg2hicanu2022-05-1730,03340,688939,705,378C:79.0%[S:73.2%,D:5.8%],F:12.1%,M:8.9%,n:1013Q53.2-C100.0(HiFi)
qqParStyg2hicanu.purging2022-05-1733,99929,833780,336,522C:79.1%[S:76.2%,D:2.9%],F:11.9%,M:9.0%,n:1013Q52.6-C87.2(HiFi)
qqParStyg2hifiasm2024-01-27535,7813,7531,043,956,624C:95.1%[S:90.2%,D:4.9%],F:3.3%,M:1.6%,n:1013Q51.1-C98.7(HiFi)
qqParStyg2hifiasm.purging2024-01-27546,7303,3141,023,786,246C:95.1%[S:90.3%,D:4.8%],F:3.3%,M:1.6%,n:1013Q51.1-C98.7(HiFi)
qqParStyg2hifiasm.scaffolding.yahs2024-01-27343,00012,084499,0008,9131,024,420,446C:92.8%[S:88.1%,D:4.7%],F:4.8%,M:2.4%,n:1013Q51.1-C98.7(HiFi)
qqParStyg2hifiasm2023-01-31295,5136,2041,024,231,623C:93.8%[S:89.3%,D:4.5%],F:3.8%,M:2.4%,n:1013Q51.6-C98.2(HiFi)
qqParStyg2hifiasm.purging2023-01-31299,0915,8661,011,237,880C:93.8%[S:89.4%,D:4.4%],F:3.8%,M:2.4%,n:1013Q51.6-C98.2(HiFi)
qqParStyg2hifiasm.scaffolding_newhic2.yahs2023-01-31134,35613,4671,011,237,880C:90.3%[S:86.2%,D:4.1%],F:6.3%,M:3.4%,n:1013Q51.6-C100.0(HiFi)
qqParStyg2hifiasm.scaffolding_newhic.yahs2023-01-31134,35613,4671,011,237,880C:90.3%[S:86.2%,D:4.1%],F:6.3%,M:3.4%,n:1013Q51.6-C98.2(HiFi)
qqParStyg2hifiasm.scaffolding.salsa2023-01-31297,4755,895299,8555,8631,011,253,880C:93.8%[S:89.4%,D:4.4%],F:3.8%,M:2.4%,n:1013Q51.6-C98.2(HiFi)
qqParStyg2hifiasm.scaffolding.yahs2023-01-31186,0009,9791,011,237,880C:92.6%[S:88.5%,D:4.1%],F:4.8%,M:2.6%,n:1013Q51.6-C98.2(HiFi)
qqParStyg2hifiasm2022-05-1744,62124,855845,527,588C:82.7%[S:79.6%,D:3.1%],F:9.2%,M:8.1%,n:1013Q50.1-C87.9(HiFi)
qqParStyg2hifiasm.purging2022-05-1744,22423,321799,307,677C:82.5%[S:79.5%,D:3.0%],F:9.2%,M:8.3%,n:1013Q50.1-C87.7(HiFi)
qqParStyg2hifiasm.scaffolding.salsa2022-05-1744,22423,32144,37623,278799,329,177C:82.5%[S:79.5%,D:3.0%],F:9.2%,M:8.3%,n:1013Q50.1-C87.7(HiFi)
qqParStyg2hifiasm.scaffolding.yahs2022-05-1742,04025,52442,04725,523799,307,877C:81.6%[S:78.7%,D:2.9%],F:9.6%,M:8.8%,n:1013Q50.1-C87.7(HiFi)
qqParStyg2hicanu2023-01-31169,37126,3841,349,980,724C:94.4%[S:80.2%,D:14.2%],F:3.8%,M:1.8%,n:1013Q51.9-C100.0(HiFi)
qqParStyg2hicanu.purging2023-01-31242,6337,3951,018,766,200C:94.3%[S:90.0%,D:4.3%],F:3.8%,M:1.9%,n:1013Q51.1-C98.8(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
qqParStyg2mitohifi.readsmito2022-05-1714,36431NoneTrueNC_044099.1; 14,220 bp; 37 genes
qqParStyg2mitohifi.hifiasmmito2024-01-2711,98627COX1FalseNC_044099.1; 14,220 bp; 37 genes
qqParStyg2mitohifi.hifiasmmito2023-01-3114,42531NoneTrueNC_044099.1; 14,220 bp; 37 genes
qqParStyg2mitohifi.hifiasmmito2022-05-1714,36431NoneTrueNC_044099.1; 14,220 bp; 37 genes
qqParStyg2mitohifi.hicanumito2023-01-3114,37032NoneTrueNC_044099.1; 14,220 bp; 37 genes
WTSI

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