Tree of Life QC

Info

NCBI taxon id: 997551
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Xyleninae;Mesoligia;
GoaT genome size (M): 655 (ancestor)
GoaT asm span (M): 889 (direct)
GoaT chr no.: 31 (ancestor)
ToLID prefix: ilMesFuru

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
ilMesFuru1Ox000519UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7701374SAMEA7701289
ilMesFuru2NHMUK010635087NATURAL HISTORY MUSEUMNOT_COLLECTEDABDOMENSAMEA7849285SAMEA7849229
ilMesFuru2NHMUK010635087NATURAL HISTORY MUSEUMNOT_COLLECTEDTHORAXSAMEA7849286SAMEA7849229
ilMesFuru2NHMUK010635087NATURAL HISTORY MUSEUMNOT_COLLECTEDHEADSAMEA7849286SAMEA7849229
ilMesFuru3Ox000520UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA8603366SAMEA8603120
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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
10xilMesFuru13130.64956,612,22851.292.8098.240.42
pacbioilMesFuru13120.46879,896,63446.332.5597.280.18
hic-arima2ilMesFuru23140.47982,053,6000.0093.931.360.23

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 - HiFiilMesFuru12021-05-1382321m64094e_210513_161115A01100111,093,071,56912,598SAMEA7701374ERR6907889
PacBio - HiFiilMesFuru12021-05-2882826m64125e_210528_144020A01100112,203,415,91913,885SAMEA7701374ERR6939247
PacBio - HiFiilMesFuru12021-07-1984559m64097e_210719_081728C01100114,900,303,93910,727SAMEA7701374ERR6808010
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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 genomeilMesFuru12021-06-1638403_2#4161,859,64224,440,805,942SAMEA7701374ERR6688574qc completeMesoligia furuncula (1.00)
Chromium genomeilMesFuru12021-06-1638403_2#3158,691,00423,962,341,604SAMEA7701374ERR6688573qc completeMesoligia furuncula (1.00)
Chromium genomeilMesFuru12021-06-1638403_2#2149,542,69222,580,946,492SAMEA7701374ERR6688572qc completeMesoligia furuncula (1.00)
Chromium genomeilMesFuru12021-06-1638403_2#1138,648,84220,935,975,142SAMEA7701374ERR6688571qc completeMesoligia furuncula (1.00)
Hi-C - Arima v2ilMesFuru22021-05-2738173_1#6697,405,418105,308,218,118SAMEA7849286ERR6688570qc completeMesoligia furuncula (1.00)
RNA PolyAilMesFuru32022-03-2544268_6#1633,379,5465,040,311,446SAMEA8603366ERR9435012qc completeMesoligia furuncula (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
0.916433NC_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
ilMesFuru1

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.

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    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    ilMesFuru1hicanu2021-06-102,076,7552,5781,792,547,481C:99.4%[S:45.9%,D:53.5%],F:0.1%,M:0.5%,n:1367-
    ilMesFuru1hicanu.purging2021-06-102,757,922674935,088,060C:99.2%[S:96.9%,D:2.3%],F:0.2%,M:0.6%,n:1367-
    ilMesFuru1hifiasm2021-06-103,375,8391,1001,739,880,608C:99.5%[S:48.1%,D:51.4%],F:0.1%,M:0.4%,n:1367-
    ilMesFuru1hifiasm.purging2021-06-105,372,497336938,443,697C:99.4%[S:95.8%,D:3.6%],F:0.1%,M:0.5%,n:1367-
    ilMesFuru1hifiasm.scaff.salsa2021-06-104,646,20144618,586,061285902,635,937-
    ilMesFuru1hifiasm.purging-noE2021-06-104,805,580424902,559,103C:99.3%[S:97.7%,D:1.6%],F:0.1%,M:0.6%,n:1367-

    Organelles

    In-progress organelle results from MitoHiFi2.

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    specimen
    asm
    date
    length
    genes
    frameshifts
    is circular
    reference
    ilMesFuru1reads2021-06-1015,35036NoneTrueNC_062119.1; 15,322 bp; 37 genes
    WTSI

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