Tree of Life QC

Info

NCBI taxon id: 2492375
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Xyleninae;Omphaloscelis;
GoaT genome size (M): 655 (ancestor)
GoaT asm span (M): 661 (direct)
GoaT chr no.: 31 (ancestor)
ToLID prefix: ilOmpLuno

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
ilOmpLuno1Ox000964UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA8603681SAMEA8603195
ilOmpLuno1Ox000964UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA8603683SAMEA8603195
ilOmpLuno1Ox000964UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA8603685SAMEA8603195
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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
10xilOmpLuno13141.31647,037,26234.431.2899.280.42
pacbioilOmpLuno13114.67650,970,44630.680.9398.170.18
hic-arima2ilOmpLuno13147.17812,645,74366.911.1896.260.43

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 - HiFiilOmpLuno12021-06-2083457m64221e_210620_060415C01101120,247,530,33714,554SAMEA8603683ERR6808005
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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
Chromium genomeilOmpLuno12021-06-2838852_2#26115,495,77417,439,861,874SAMEA8603683ERR6688541qc completeOmphaloscelis lunosa (1.00)
Chromium genomeilOmpLuno12021-06-2838852_2#28161,219,67624,344,171,076SAMEA8603683ERR6688543qc completeOmphaloscelis lunosa (1.00)
Chromium genomeilOmpLuno12021-06-2838852_2#27145,873,11022,026,839,610SAMEA8603683ERR6688542qc completeOmphaloscelis lunosa (1.00)
Chromium genomeilOmpLuno12021-06-2838852_2#25133,812,78820,205,730,988SAMEA8603683ERR6688540qc completeOmphaloscelis lunosa (1.00)
Hi-C - Arima v2ilOmpLuno12021-06-1038406_4#6718,750,568108,531,335,768SAMEA8603681ERR6688539qc completeOmphaloscelis lunosa (1.00)
RNA PolyAilOmpLuno12022-03-2544268_7#2238,649,1085,836,015,308SAMEA8603685ERR9435009qc completeOmphaloscelis lunosa (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
0.923732NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
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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
No matching records found

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
ilOmpLuno1

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

    BTK datasets:

    ilOmpLuno1_pri

    Assemblies

    In-progress assembly QC.

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    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    ilOmpLuno1hicanu2021-06-291,231,6224,3381,349,404,858C:99.3%[S:64.6%,D:34.7%],F:0.5%,M:0.2%,n:1367Q43.2-C97.0(10X)
    ilOmpLuno1hicanu.purging2021-06-298,290,026249657,064,973C:99.2%[S:98.5%,D:0.7%],F:0.5%,M:0.3%,n:1367Q50.6-C96.8(10X)
    ilOmpLuno1hifiasm2021-06-2921,574,746191683,519,114C:99.1%[S:98.3%,D:0.8%],F:0.4%,M:0.5%,n:1367Q50.7-C96.9(10X)
    ilOmpLuno1hifiasm.purging2021-06-2921,574,74660661,925,661C:99.1%[S:98.5%,D:0.6%],F:0.4%,M:0.5%,n:1367Q51.1-C96.9(10X)
    ilOmpLuno1hifiasm.scaff.salsa2021-06-2921,574,6546222,138,92157661,924,276-

    Organelles

    In-progress organelle results from MitoHiFi2.

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    specimen
    asm
    date
    length
    genes
    frameshifts
    is circular
    reference
    ilOmpLuno1reads2021-06-2915,46937NoneTrueNC_062119.1; 15,322 bp; 37 genes
    WTSI

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