Tree of Life QC

Info

NCBI taxon id: 113334
Order: Lepidoptera
Family: Nymphalidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Papilionoidea;Nymphalidae;Nymphalinae;Melitaea;
GoaT genome size (M): 440 (ancestor)
GoaT asm span (M): 449 (direct)
GoaT chr no.: 62 (direct)
ToLID prefix: ilMelCinx

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
ilMelCinx1SAN0000952SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523567SAMEA7523475
ilMelCinx2SAN0000953SANGER INSTITUTEMALEWHOLE_ORGANISMSAMEA7523568SAMEA7523476
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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
10xilMelCinx13133.18533,875,49835.332.1298.330.54
pacbioilMelCinx13113.97493,758,86827.861.9399.330.15
hic-arima2ilMelCinx13158.7633,929,24857.041.3193.480.41

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 - HiFiilMelCinx12020-05-29TRACTION-RUN-38m64016_200529_142754B01100314,501,861,95613,441SAMEA7523567ERR6576320
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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 genomeilMelCinx12020-09-0935001_7#685,682,65012,938,080,150SAMEA7523567ERR6054429qc completeMelitaea cinxia (1.00)
Chromium genomeilMelCinx12020-09-0935001_7#876,524,95011,555,267,450SAMEA7523567ERR6054431qc completeMelitaea cinxia (1.00)
Chromium genomeilMelCinx12020-09-0935001_7#7136,446,13620,603,366,536SAMEA7523567ERR6054430qc completeMelitaea cinxia (1.00)
Chromium genomeilMelCinx12020-09-0935001_7#583,810,63612,655,406,036SAMEA7523567ERR6054428qc completeMelitaea cinxia (1.00)
Hi-C - Arima v2ilMelCinx12020-11-1435430_1#3699,289,272105,592,680,072SAMEA7523567ERR6054432qc completeMelitaea cinxia (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
0.937001NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.906747NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.906409[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.905724[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.905377NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.903605[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.902135[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.

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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
ilMelCinx1

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
    ilMelCinx1hifiasm.purging2020-10-187,977,926114504,271,934C:98.0%[S:97.3%,D:0.7%],F:0.4%,M:1.6%,n:1658-
    ilMelCinx1hifiasm2020-10-185,316,826258675,596,090C:98.0%[S:72.7%,D:25.3%],F:0.5%,M:1.5%,n:1658-
    ilMelCinx1hifiasm.purge2.polish1.scaff1.salsa2020-10-187,977,87611615,579,11173504,290,924-
    ilMelCinx1hifiasm.purge2.polish1.scaff12020-10-187,977,87611416,149,26970504,291,424-
    ilMelCinx1hifiasm.purging22020-10-187,977,926114504,271,934-
    ilMelCinx1hicanu.purging2020-10-183,730,158226499,656,737C:98.4%[S:98.0%,D:0.4%],F:0.4%,M:1.2%,n:1658-
    ilMelCinx1hicanu2020-10-182,533,7971,476970,498,615C:98.1%[S:18.6%,D:79.5%],F:0.4%,M:1.5%,n:1658-
    ilMelCinx1hicanu.purge2.polish1.scaff1.salsa2020-10-183,730,16222612,590,433136499,684,097-
    ilMelCinx1hicanu.purge2.polish1.scaff12020-10-183,730,16222513,715,264137499,683,097-
    ilMelCinx1hicanu.purging22020-10-183,730,158225499,640,351-

    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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