Tree of Life QC

Info

NCBI taxon id: 55057
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Hadeninae;Mamestra;
GoaT genome size (M): 586 (ancestor)
GoaT asm span (M): 576 (direct)
GoaT chr no.: 62 (direct)
ToLID prefix: ilMamBras

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
ilMamBras1SAN0001209SANGER INSTITUTEMALEMID_BODYSAMEA7524189SAMEA7524129
ilMamBras1SAN0001209SANGER INSTITUTEMALEMID_BODYSAMEA7524188SAMEA7524129
ilMamBras1SAN0001209SANGER INSTITUTEMALEHEADSAMEA7524186SAMEA7524129
ilMamBras1SAN0001209SANGER INSTITUTEMALEPOSTERIOR_BODYSAMEA7524190SAMEA7524129
ilMamBras1SAN0001209SANGER INSTITUTEMALEMID_BODYSAMEA7524187SAMEA7524129
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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
10xilMamBras13130.69618,401,00527.660.0197.240.48
pacbioilMamBras13117.27573,463,74121.270.0598.640.16
hic-arima2ilMamBras13191.15312,944,81032.3418.5296.510.47

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 - HiFiilMamBras12020-07-1176634m64097_200711_164440C01100220,884,861,60411,654SAMEA7524188ERR6412357
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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 genomeilMamBras12020-10-0835147_5#5108,108,78216,324,426,082SAMEA7524188ERR6002681qc completeMamestra brassicae (1.00)
Chromium genomeilMamBras12020-10-0835147_5#796,378,27014,553,118,770SAMEA7524188ERR6002683qc completeMamestra brassicae (1.00)
Chromium genomeilMamBras12020-10-0835147_5#6123,147,98418,595,345,584SAMEA7524188ERR6002682qc completeMamestra brassicae (1.00)
Chromium genomeilMamBras12020-10-0835147_5#874,050,16411,181,574,764SAMEA7524188ERR6002684qc completeMamestra brassicae (1.00)
Hi-C - Arima v2ilMamBras12020-09-0834957_3#5184,640,17627,880,666,576SAMEA7524188ERR6002678qc completeMamestra brassicae (1.00)
Hi-C - Arima v2ilMamBras12020-09-0834957_4#5184,159,38827,808,067,588SAMEA7524188ERR6002679qc completeMamestra brassicae (1.00)
Hi-C - Arima v2ilMamBras12020-09-0834957_5#5183,000,45027,633,067,950SAMEA7524188ERR6002680qc completeMamestra brassicae (1.00)
RNA PolyAilMamBras42021-09-1740838_6#832,285,4184,875,098,118SAMEA7524198ERR6787417qc completeMamestra brassicae (1.00)
RNA PolyAilMamBras22021-03-1936703_4#1748,590,3047,337,135,904SAMEA7524192ERR6002685qc completeMamestra brassicae (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
0.918565NC_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
ilMamBras1

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
    ilMamBras1hifiasm.purging2020-10-1517,758,57567576,205,850C:98.2%[S:97.2%,D:1.0%],F:0.7%,M:1.1%,n:1658-
    ilMamBras1hifiasm2020-10-1517,758,575105578,449,601C:98.2%[S:97.3%,D:0.9%],F:0.6%,M:1.2%,n:1658-
    ilMamBras1hifiasm.scaffolding.salsa2020-10-1517,758,5546919,384,29655576,211,909-
    ilMamBras1hifiasm.scaffolding2020-10-1517,758,5546719,384,29653576,211,909-
    ilMamBras1hicanu2020-10-1511,440,6954,019687,350,845C:98.2%[S:85.5%,D:12.7%],F:0.5%,M:1.3%,n:1658-
    ilMamBras1hicanu.purging2020-10-1513,926,417114576,029,690C:98.2%[S:97.3%,D:0.9%],F:0.5%,M:1.3%,n:1658-

    Organelles

    In-progress organelle results from MitoHiFi2.

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    specimen
    asm
    date
    length
    genes
    frameshifts
    is circular
    reference
    No matching records found
    WTSI

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