Tree of Life QC

Info

NCBI taxon id: 1660671  NCBI; ENA; GoaT
Order: Lepidoptera
Family: Tortricidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Tortricoidea;Tortricidae;Olethreutinae;Grapholitini;Pammene;
GoaT genome size (M): 600 (ancestor)
GoaT asm span (M): 803 (ancestor)
GoaT chr no.: 28 (ancestor)
GoaT haploid no.: 28 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: ilPamRegi

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
ilPamRegi1Ox000656UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7701700SAMEA7701518
ilPamRegi2NHMUK013697073NATURAL HISTORY MUSEUMNOT_COLLECTEDTHORAXSAMEA115599778SAMEA115574683
ilPamRegi2NHMUK013697073NATURAL HISTORY MUSEUMNOT_COLLECTEDABDOMENSAMEA115575071SAMEA115574683
ilPamRegi3LUNDPSY000043Lund UniversityNOT_COLLECTEDWHOLE_ORGANISMSAMEA116130068SAMEA116129970
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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
pacbioilPamRegi13128.23773,998,06046.340.8595.790.13
histogram.txt
10xilPamRegi13121.21906,506,02353.800.6399.030.34
histogram.txt
hic-arima2ilPamRegi23124.21,513,552,55398.711.7797.410.36
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 - HiFiilPamRegi12021-03-2680865m64222e_210326_144844B01100919,161,343,25715,031SAMEA7701700ERR12370359
PacBio - HiFiilPamRegi12021-08-3086028m64016e_210830_045338C0110092,738,655,13713,122SAMEA7701700ERR12370358
PacBio - HiFi (ULI)ilPamRegi12022-02-26TRACTION-RUN-73m64016e_220226_181552C01-23,716,756,6639,814SAMEA7701700ERR12370357
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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 genomeilPamRegi12021-04-0637204_4#2467,996,43210,267,461,232SAMEA7701700ERR12374339qc complete
Chromium genomeilPamRegi12021-04-0637204_4#2391,940,92813,883,080,128SAMEA7701700ERR12374338qc completePammene regiana (1.00)
Chromium genomeilPamRegi12021-04-0637204_4#22108,104,32016,323,752,320SAMEA7701700ERR12374337qc completePammene regiana (1.00)
Chromium genomeilPamRegi12021-04-0637204_4#21119,542,94418,050,984,544SAMEA7701700ERR12374336qc completePammene regiana (1.00)
Hi-C - Arima v2ilPamRegi22024-09-1649524_2#4683,428,642103,197,724,942SAMEA115599778ERR13702753qc completePammene regiana (1.00)
RNA PolyAilPamRegi22024-11-1949828_8#6675,671,35611,426,374,756SAMEA115575071qc completePammene regiana (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
0.993336[43 seqs] NZ_JQAM01000001.1 Wolbachia pipientis strain wRec s1, whole genome shotgun sequence [...]
0.940376[256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...]
0.922553NC_013521.1 Sanguibacter keddieii DSM 10542, complete genome
0.914483NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
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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
ilPamRegi1atg004002l1907
  • 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;
ilPamRegi1atg004575l1922
  • 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;
ilPamRegi1ptg000055c1500
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia;
  • SILVA: Bacteria;Pseudomonadota;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
ilPamRegi1ptg000111l1211
  • ENA: Bacteria;
  • SILVA: Bacteria;Pseudomonadota;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
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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
ilPamRegi1Anaplasmataceae80,7421.97C:99.7%[S:0.0%,D:99.7%],F:0.0%,M:0.3%,n:364C:99.5%[S:0.3%,D:99.2%],F:0.0%,M:0.5%,n:364744.48Mb79,909C:99.5%[S:0.3%,D:99.2%],F:0.0%,M:0.5%,n:36453.28Mb80,835
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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
ilPamRegi1

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

  • ilPamRegi1.hifiasm.20240916

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
ilPamRegi1hifiasm.purging2024-09-1616,725,442114857,126,476C:98.9%[S:98.0%,D:0.9%],F:0.4%,M:0.7%,n:1367Q52.4-C96.6(10X); Q63.2-C98.2(HiFi)
ilPamRegi1hifiasm.scaffolding.yahs2024-09-169,545,65919729,929,40078857,150,276C:99.0%[S:98.3%,D:0.7%],F:0.4%,M:0.6%,n:1367Q52.4-C96.6(10X); Q63.2-C98.2(HiFi)
ilPamRegi1hifiasm2024-09-1616,322,886485908,570,133C:98.8%[S:96.1%,D:2.7%],F:0.4%,M:0.8%,n:1367Q51.7-C96.9(10X); Q61.9-C98.5(HiFi)
ilPamRegi1hifiasm.scaffolding_alt.yahs2024-09-16320,0657,63417,889,2505,115749,752,413C:77.4%[S:72.6%,D:4.8%],F:2.0%,M:20.6%,n:1367Q50.9-C96.9(10X); Q59.3-C98.5(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
ilPamRegi1mitohifi.readsmito2024-09-1616,50537NoneTrue1PP776023.1; 15,488 bp; 37 genes
ilPamRegi1mitohifi.hifiasmmito2024-09-1616,82937NoneTrue1PP776023.1; 15,488 bp; 37 genes
WTSI

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