Tree of Life QC

Info

NCBI taxon id: 1660692
Order: Lepidoptera
Family: Pterophoridae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Pterophoroidea;Pterophoridae;Pterophorinae;Stenoptilia;
GoaT genome size (M): 555 (ancestor)
GoaT asm span (M): 822 (direct)
GoaT chr no.: 56 (ancestor)
ToLID prefix: ilSteBipu

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
ilSteBipu1Ox001799UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA10979452SAMEA10979057
ilSteBipu2Ox001800UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA10979453SAMEA10979058
ilSteBipu3Ox001801UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA10979454SAMEA10979059
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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
pacbioilSteBipu13111.91844,629,99647.083.1697.840.10
hic-arima2ilSteBipu23167.23791,405,81064.336.1296.620.54

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 (mplx)ilSteBipu12022-04-25TRACTION-RUN-99m64221e_220425_075716C01100220,814,955,06311,894SAMEA10979452ERR9836416
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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 v2ilSteBipu22022-04-0644475_3#11,039,058,726156,897,867,626SAMEA10979453ERR9793170qc completeStenoptilia bipunctidactyla (1.00)
RNA PolyAilSteBipu32022-08-2345657_1#7963,785,2749,631,576,374SAMEA10979454qc completeStenoptilia bipunctidactyla (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
0.931235NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.901381[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
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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
ilSteBipu1atg000017l684
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000026l707
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Lepidoptera;Glossata;Ditrysia;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000029l692
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000052l681
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000078l689
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000090l681
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000125l688
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000169l674
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1atg000372l687
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilSteBipu1ptg000009l658
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
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102550
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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
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
ilSteBipu1

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

  • ilSteBipu1.hifiasm.20220427

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
ilSteBipu1hifiasm-hic2022-04-272,834,3751,0291,463,921,689C:99.5%[S:26.7%,D:72.8%],F:0.1%,M:0.4%,n:1367Q66.0-C99.3(HiFi)
ilSteBipu1hicanu2022-04-271,768,3552,7931,659,527,111C:99.5%[S:4.4%,D:95.1%],F:0.1%,M:0.4%,n:1367Q74.1-C100.0(HiFi)
ilSteBipu1hicanu.purging2022-04-272,205,6111,195926,022,849C:99.1%[S:89.6%,D:9.5%],F:0.3%,M:0.6%,n:1367Q76.1-C99.2(HiFi)
ilSteBipu1hifiasm.scaff_e.salsa2022-04-273,496,97367512,473,284434846,756,606-
ilSteBipu1hifiasm.scaff_e.yahs2022-04-273,665,53171727,163,460340846,711,506C:99.3%[S:96.7%,D:2.6%],F:0.1%,M:0.6%,n:1367Q65.4-C99.1(HiFi)
ilSteBipu1hifiasm.purging_e2022-04-273,709,0536253,995,344527846,638,360-
ilSteBipu1hifiasm.purging2022-04-273,967,569535899,284,521C:99.4%[S:90.4%,D:9.0%],F:0.1%,M:0.5%,n:1367Q65.6-C99.2(HiFi)
ilSteBipu1hifiasm.purging_calcuts_202022-04-273,979,811525896,806,245-
ilSteBipu1hifiasm2022-04-272,870,4141,0271,460,239,841C:99.5%[S:27.5%,D:72.0%],F:0.1%,M:0.4%,n:1367Q65.8-C99.3(HiFi)
ilSteBipu1hifiasm.scaffolding.salsa2022-04-273,665,53160114,829,962379899,395,521C:99.4%[S:91.5%,D:7.9%],F:0.1%,M:0.5%,n:1367Q65.6-C99.2(HiFi)
ilSteBipu1hifiasm.scaffolding.yahs2022-04-273,693,56764027,909,523288899,354,921C:99.3%[S:92.0%,D:7.3%],F:0.1%,M:0.6%,n:1367Q65.6-C99.2(HiFi)

Organelles

In-progress organelle results from MitoHiFi2.

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specimen
asm
date
length
genes
frameshifts
is circular
reference
ilSteBipu1hicanu2022-04-2717,81236NoneTrueNC_062712.1; 15,402 bp; 37 genes
ilSteBipu1reads2022-04-2717,81436NoneTrueNC_062712.1; 15,402 bp; 37 genes
ilSteBipu1hifiasm2022-04-2717,81436NoneTrueNC_062712.1; 15,402 bp; 37 genes
WTSI

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