Tree of Life QC

Info

NCBI taxon id: 988106  NCBI; ENA; GoaT
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Xyleninae;Dryobotodes;
GoaT genome size (M): 655 (ancestor)
GoaT asm span (M): 709 (direct)
GoaT chr no.: 31 (ancestor)
GoaT haploid no.: 30 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: ilDryErem

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
ilDryErem1Ox000959UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA8603659SAMEA8603190
ilDryErem1Ox000959UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA8603661SAMEA8603190
ilDryErem1Ox000959UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA8603657SAMEA8603190
Showing 1 to 3 of 3 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
10xilDryErem13127.28748,317,27141.041.9698.650.42
histogram.txt
pacbioilDryErem13113.86676,618,58433.761.8298.440.21
histogram.txt
hic-arima2ilDryErem13143.56711,572,25269.397.4097.410.41
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 - HiFiilDryErem12021-06-2483712m64097e_210624_133939A01102220,063,776,48716,021SAMEA8603659ERR6808003
Showing 1 to 1 of 1 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
Chromium genomeilDryErem12021-06-2838852_2#688,814,56213,410,998,862SAMEA8603659ERR6688526qc completeDryobotodes eremita (1.00)
Chromium genomeilDryErem12021-06-2838852_2#896,462,18814,565,790,388SAMEA8603659ERR6688528qc completeDryobotodes eremita (1.00)
Chromium genomeilDryErem12021-06-2838852_2#5103,418,93015,616,258,430SAMEA8603659ERR6688525qc completeDryobotodes eremita (1.00)
Chromium genomeilDryErem12021-06-2838852_2#7135,953,57620,528,989,976SAMEA8603659ERR6688527qc completeDryobotodes eremita (1.00)
Hi-C - Arima v2ilDryErem12021-06-1038406_4#1576,738,59087,087,527,090SAMEA8603657ERR6688524qc completeDryobotodes eremita (1.00)
RNA PolyAilDryErem12022-03-2544268_7#836,639,1885,532,517,388SAMEA8603661ERR9435006qc completeDryobotodes eremita (1.00)
Showing 1 to 6 of 6 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
0.924195NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.900615[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
Showing 1 to 2 of 2 rows

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

Loading, please wait
specimen
contig
SSU length
attributed taxonomy by SSU
No matching records found

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
No matching records found

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

Loading, please wait
specimen
visualisation
ilDryErem1

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

    Assemblies

    In-progress assembly QC.

    Loading, please wait
    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    ilDryErem1hicanu2021-06-292,862,2512,2031,431,690,763C:99.4%[S:52.2%,D:47.2%],F:0.4%,M:0.2%,n:1367Q46.5-C97.3(10X)
    ilDryErem1hicanu.purging2021-06-295,835,548310719,078,692C:99.1%[S:98.1%,D:1.0%],F:0.4%,M:0.5%,n:1367Q54.0-C97.2(10X)
    ilDryErem1hifiasm2021-06-2922,539,152308750,093,808C:99.2%[S:98.7%,D:0.5%],F:0.4%,M:0.4%,n:1367Q52.4-C97.3(10X)
    ilDryErem1hifiasm.purging2021-06-2922,620,556102715,757,663C:99.2%[S:98.8%,D:0.4%],F:0.4%,M:0.4%,n:1367Q55.3-C97.2(10X)
    ilDryErem1hifiasm.scaff.salsa2021-06-2922,620,48311423,146,544102715,759,862-

    Organelles

    In-progress organelle results from MitoHiFi or Oatk.

    Loading, please wait
    specimen
    asm
    organelle
    date
    length
    genes
    frameshifts
    is circular
    reference
    No matching records found
    WTSI

    Tree of Life Species Report is developed within the Tree of Life Programme at the Wellcome Sanger Institute
    Copyright © 2020-2024 Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457.
    Terms and conditions | Cookies policy.