Tree of Life QC

Info

NCBI taxon id: 64459
Order: Lepidoptera
Family: Pieridae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Papilionoidea;Pieridae;Pierinae;Pieris;
GoaT genome size (M): 254 (ancestor)
GoaT asm span (M): 245 (direct)
GoaT chr no.: 50 (direct)
GoaT ploidy: 2 (ancestor)
ToLID prefix: ilPieRapa

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
ilPieRapa1SAN0000822SANGER INSTITUTEFEMALEWHOLE_ORGANISMSAMEA7523264SAMEA7523164
ilPieRapa2SAN20001350SANGER INSTITUTEMALEHEADSAMEA111436085SAMEA111436077
ilPieRapa2SAN20001350SANGER INSTITUTEMALETHORAXSAMEA111436083SAMEA111436077
ilPieRapa2SAN20001350SANGER INSTITUTEMALESPERM_SEMINAL_FLUIDSAMEA111436104SAMEA111436077
ilPieRapa3SAN20001347SANGER INSTITUTEMALEHEADSAMEA111436084SAMEA111436078
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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-arimailPieRapa13151.47515,713,6830.00100.001.570.26
10xilPieRapa13178.75265,944,55921.532.1193.410.51
pacbioilPieRapa13127.26247,937,47113.581.9999.000.22

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 - HiFiilPieRapa12019-12-23TRACTION-RUN-4m64016_191223_193312A01101814,514,763,06714,192SAMEA7523264ERR6606787
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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 - Arima v1ilPieRapa12020-03-2533892_7#1476,181,97271,903,477,772SAMEA7523264ERR6002748qc completePieris rapae (1.00)
Chromium genomeilPieRapa12020-02-0432955_5#796,942,24414,638,278,844SAMEA7523264ERR6002746qc completePieris rapae (1.00)
Chromium genomeilPieRapa12020-02-0432955_5#6117,528,96217,746,873,262SAMEA7523264ERR6002745qc completePieris rapae (1.00)
Chromium genomeilPieRapa12020-02-0432955_5#8145,700,07622,000,711,476SAMEA7523264ERR6002747qc completePieris rapae (1.00)
Chromium genomeilPieRapa12020-02-0432955_5#586,049,57212,993,485,372SAMEA7523264ERR6002744qc completePieris rapae (1.00)
RNA PolyAilPieRapa12021-05-2537935_7#1632,565,2204,917,348,220SAMEA7523264ERR6286709qc completePieris rapae (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
0.931037NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.907083[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.904322[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.903605NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.900615[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
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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
ilPieRapa1

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
    canuccs.purge2020-01-1510,943,8176210,943,81753256,312,092C:98.7%[S:98.4%,D:0.3%],F:0.3%,M:1.0%,n:1658-
    falconccs.2-asm-falcon2020-01-039,422,358629,422,35855256,212,453C:98.6%[S:98.1%,D:0.5%],F:0.4%,M:1.0%,n:1658-

    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

    Tree of Life Species Report is developed within the Tree of Life Programme at the Wellcome Sanger Institute
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