Tree of Life QC

Info

NCBI taxon id: 272628
Order: Lepidoptera
Family: Hesperiidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Hesperioidea;Hesperiidae;Hesperiinae;Hesperiini;Thymelicus;
GoaT genome size (M): 555 (ancestor)
GoaT asm span (M): 470 (direct)
GoaT chr no.: 54 (direct)
ToLID prefix: ilThySylv

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
ilThySylv1SAN0000837SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523375SAMEA7523279
ilThySylv2SAN0000838SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523376SAMEA7523280
ilThySylv3SAN0000839SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523377SAMEA7523281
ilThySylv4SAN0000840SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523378SAMEA7523282
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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
hic-qiagenilThySylv13138.96660,652,2330.00100.005.490.13
10xilThySylv13131.65511,780,19544.581.6998.950.65
hic-arima2ilThySylv33199.6427,335,33052.844.5797.610.45

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 - HiFiilThySylv12019-12-24TRACTION-RUN-3m64097_191224_194147B01101820,157,774,29812,242SAMEA7523375ERR6608659
PacBio - IsoSeqilThySylv22022-03-19TRACTION-RUN-75m64089e_220319_103806C0110031,262,601,2651,867SAMEA7523376
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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
Hi-C - QiagenilThySylv12020-03-2633893_6#1442,314,07066,789,424,570SAMEA7523375qc completeThymelicus sylvestris (1.00)
Chromium genomeilThySylv12020-03-0633610_7#379,593,84612,018,670,746SAMEA7523375ERR6363312qc completeThymelicus sylvestris (1.00)
Chromium genomeilThySylv12020-03-0633610_7#1107,272,41216,198,134,212SAMEA7523375ERR6363310qc completeThymelicus sylvestris (1.00)
Chromium genomeilThySylv12020-03-0633610_7#292,339,80813,943,311,008SAMEA7523375ERR6363311qc completeThymelicus sylvestris (1.00)
Chromium genomeilThySylv12020-03-0633610_7#482,987,14812,531,059,348SAMEA7523375ERR6363313qc completeThymelicus sylvestris (1.00)
Hi-C - Arima v2ilThySylv32021-05-2738173_2#8801,878,106121,083,594,006SAMEA7523377ERR6363315qc completeThymelicus sylvestris (1.00)
RNA PolyAilThySylv22021-05-2537935_5#1938,385,8905,796,269,390SAMEA7523376ERR6363314qc completeThymelicus sylvestris (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
0.999329[120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...]
0.919849NC_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
ilThySylv1

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
    ilThySylv1hifiasm.purging_e2021-05-2716,949,4359516,949,43589472,667,032-
    ilThySylv1hifiasm.purging2021-05-2716,949,43589472,814,601C:98.6%[S:98.2%,D:0.4%],F:0.4%,M:1.0%,n:1367Q47.9-C95.7(10X); Q64.0-C99.2(HiFi)
    ilThySylv1hifiasm2021-05-2716,606,612330487,366,605C:98.7%[S:97.6%,D:1.1%],F:0.4%,M:0.9%,n:1367Q45.6-C95.7(10X); Q60.6-C99.2(HiFi)
    ilThySylv1hifiasm.scaff.salsa2021-05-2716,606,5509217,253,31977472,820,864-
    ilThySylv1hifiasm.purging2020-09-0414,817,383107473,437,433-
    ilThySylv1hifiasm.ilThySylv1.PB.asm2.purge1.polish1.scaff1.salsa2020-09-0414,817,365112473,436,126-
    ilThySylv1hifiasm.ilThySylv1.PB.asm2.purge1.polish1.scaff12020-09-0414,817,365107473,436,126-
    falconccs.2-asm-falcon2020-01-033,000,9593073,239,664258471,893,477C:97.7%[S:96.6%,D:1.1%],F:0.7%,M:1.6%,n:1658-
    ilThySylv1hicanu.purging2020-09-034,025,691294473,471,811-
    ilThySylv1hicanu.ilThySylv1.PB.asm1.purge1.polish1.scaff1.salsa2020-09-034,025,6833274,025,683326473,471,632-
    ilThySylv1hicanu.ilThySylv1.PB.asm1.purge1.polish1.scaff12020-09-034,025,6832944,025,683293473,471,632-
    ilThySylv1hicanu2021-05-272,182,1471,942951,856,495C:98.9%[S:51.6%,D:47.3%],F:0.3%,M:0.8%,n:1367Q44.5-C95.7(10X); Q72.0-C99.3(HiFi)
    ilThySylv1hicanu.purging2021-05-274,025,691294473,471,811C:98.8%[S:98.2%,D:0.6%],F:0.4%,M:0.8%,n:1367Q48.2-C95.7(10X); Q73.1-C99.2(HiFi)

    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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