Tree of Life QC

Info

NCBI taxon id: 201766  NCBI; ENA; GoaT
Order: Coleoptera
Family: Attelabidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Coleoptera;Polyphaga;Cucujiformia;Attelabidae;Apoderinae;Apoderus;
GoaT genome size (M): 978 (ancestor)
GoaT asm span (M): 428 (direct)
GoaT chr no.: 28 (direct)
GoaT haploid no.: 14 (direct)
GoaT ploidy: 2 (direct)
ToLID prefix: icApoCory

Specimens

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

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tolid
specimen_id
gal
sex
organism_part
biosample
biospecimen
icApoCory1Ox000474UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7520780SAMEA7520690
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Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
10xicApoCory13141.24451,870,25545.251.1697.440.55
histogram.txt
pacbioicApoCory13129.57419,170,82140.081.0497.490.15
histogram.txt
hic-arima2icApoCory13181.79554,401,15670.061.1196.020.40
histogram.txt

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 - HiFiicApoCory12020-09-2777511m64097_200927_155741D01101526,044,077,88511,910SAMEA7520780ERR6412370
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ONT run data

Below are stats for each ONT seqeuncing run collected for this species.

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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.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Chromium genomeicApoCory12020-10-1935210_8#280,179,12212,107,047,422SAMEA7520780ERR6054773qc completeApoderus coryli (1.00)
Chromium genomeicApoCory12020-10-1935210_8#1119,070,90417,979,706,504SAMEA7520780ERR6054772qc completeApoderus coryli (1.00)
Chromium genomeicApoCory12020-10-1935210_8#3100,512,36615,177,367,266SAMEA7520780ERR6054774qc completeApoderus coryli (1.00)
Chromium genomeicApoCory12020-10-1935210_8#4103,695,76015,658,059,760SAMEA7520780ERR6054775qc completeApoderus coryli (1.00)
Hi-C - Arima v2icApoCory12020-10-1335199_2#1848,663,590128,148,202,090SAMEA7520780ERR6054771qc completeApoderus coryli (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
0.967069[256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...]
0.935035NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.907083NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.904322[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.901381[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.900227[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

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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.

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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.

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specimen
visualisation
icApoCory1

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
    icApoCory1hicanu2020-10-151,902,1252,862869,365,829C:99.4%[S:13.6%,D:85.8%],F:0.2%,M:0.4%,n:1658-
    icApoCory1hicanu.purging2020-10-158,495,528272425,970,747C:99.4%[S:97.3%,D:2.1%],F:0.5%,M:0.1%,n:1658-
    icApoCory1hicanu.scaff.salsa2020-10-158,495,50327919,168,573197426,009,477-
    icApoCory1hicanu.scaff2020-10-158,495,50327220,662,949188426,010,477-
    icApoCory1hifiasm2020-10-1514,577,625711460,578,784C:99.4%[S:97.0%,D:2.4%],F:0.6%,M:0.0%,n:1658-
    icApoCory1hifiasm.purging2020-10-1515,031,097201431,672,085C:99.3%[S:97.3%,D:2.0%],F:0.6%,M:0.1%,n:1658-
    icApoCory1hifiasm.scaff.salsa2020-10-1515,031,10620918,993,748177431,685,186-
    icApoCory1hifiasm.scaff2020-10-1515,031,10620122,273,614171431,684,186-

    Organelles

    In-progress organelle results from MitoHiFi or Oatk.

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

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