Tree of Life QC

Info

NCBI taxon id: 875880
Order: Lepidoptera
Family: Erebidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Erebidae;Arctiinae;Spilosoma;
GoaT genome size (M): 625 (ancestor)
GoaT asm span (M): 587 (direct)
GoaT chr no.: 60 (direct)
ToLID prefix: ilSpiLubr

Specimens

Below is information about specimens collected for this species retrieved from the Golden Record manifest.

Loading, please wait
public_name
specimen_id
gal
sex
organism_part
biosample
biospecimen
ilSpiLubr1Ox000402UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7520617SAMEA7520525
ilSpiLubr1Ox000402UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7520616SAMEA7520525
ilSpiLubr1Ox000402UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA7520616SAMEA7520525
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 GenomeScope.

Loading, please wait
source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
10xilSpiLubr13118.96634,188,21831.761.9099.120.53
pacbioilSpiLubr13119.57585,807,98125.711.8098.530.17
hic-arima2ilSpiLubr13150.87876,842,08857.630.7694.660.55

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 - HiFiilSpiLubr12020-09-1077368m64089_200910_153732A01101624,244,080,28910,768SAMEA7520617ERR6406203
Showing 1 to 1 of 1 rows

Illumina run data

Illumina run stats.

Loading, please wait
pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Chromium genomeilSpiLubr12020-11-1635281_5#453,716,0388,111,121,738SAMEA7520617ERR6054442qc completeSpilosoma lubricipeda (1.00)
Chromium genomeilSpiLubr12020-11-1635281_5#274,543,85011,256,121,350SAMEA7520617ERR6054440qc completeSpilosoma lubricipeda (1.00)
Chromium genomeilSpiLubr12020-11-1635281_5#171,799,04410,841,655,644SAMEA7520617ERR6054439qc completeSpilosoma lubricipeda (1.00)
Chromium genomeilSpiLubr12020-11-1635281_5#359,112,4808,925,984,480SAMEA7520617ERR6054441qc completeSpilosoma lubricipeda (1.00)
Hi-C - Arima v2ilSpiLubr12020-10-2835275_8#1874,297,052132,018,854,852SAMEA7520617ERR6054438qc completeSpilosoma lubricipeda (0.99)
RNA PolyAilSpiLubr12022-03-2544268_6#431,340,2804,732,382,280SAMEA7520616ERR9434968qc completeSpilosoma lubricipeda (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
0.934114NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.906747[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.903605[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...]
0.902507[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.902135NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
Showing 1 to 5 of 5 rows

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

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

Re-assembly of reads classified under each identified SSU Marker family.

Loading, please wait
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.

Loading, please wait
specimen
visualisation
ilSpiLubr1

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
    ilSpiLubr1hifiasm2020-10-2421,050,909202616,962,558C:98.8%[S:94.2%,D:4.6%],F:0.2%,M:1.0%,n:1658-
    ilSpiLubr1hifiasm.purging2020-10-2421,028,38750587,914,284C:98.9%[S:97.5%,D:1.4%],F:0.2%,M:0.9%,n:1658-
    ilSpiLubr1hifiasm.purge.polish.scaff.salsa2020-10-2420,639,5725421,028,32452587,913,726-
    ilSpiLubr1hifiasm.purge.polish.scaff2020-10-2421,028,3245021,050,86747587,914,226-
    ilSpiLubr1hicanu.purging2020-10-2411,626,295184587,528,350C:98.8%[S:97.2%,D:1.6%],F:0.2%,M:1.0%,n:1658-
    ilSpiLubr1hicanu2020-10-242,488,2772,0271,193,412,370C:98.3%[S:9.2%,D:89.1%],F:0.3%,M:1.4%,n:1658-

    Organelles

    In-progress organelle results from MitoHiFi2.

    Loading, please wait
    specimen
    asm
    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 © 2020-2022 Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457.
    Terms and conditions | Cookies policy.