Tree of Life QC

Info

NCBI taxon id: 721163
Order: Lepidoptera
Family: Drepanidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Drepanoidea;Drepanidae;Thyatirinae;Thyatira;
GoaT genome size (M): 317 (ancestor)
GoaT asm span (M): 314 (direct)
GoaT chr no.: 62 (direct)
ToLID prefix: ilThyBati

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
ilThyBati1Ox000061UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7519960SAMEA7519923
ilThyBati1Ox000061UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7519960SAMEA7519923
ilThyBati1Ox000061UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA7519961SAMEA7519923
ilThyBati2Ox000572UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7701595SAMEA7701436
ilThyBati2Ox000572UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7701594SAMEA7701436
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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
---00.00NaNNaNNaN
hic-arimailThyBati13163.94595,925,9110.0050.111.290.25
10xilThyBati13153.8337,371,97635.372.1597.140.50
pacbioilThyBati13114.63308,594,97027.341.7897.100.21

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 - HiFiilThyBati12019-10-1672309m64016_191016_110433A0110039,655,227,34612,978SAMEA7519960ERR6608652
PacBio - IsoSeqilThyBati22021-09-04TRACTION-RUN-63m64222e_210904_144241B0110041,316,170,6423,437SAMEA7701595
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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 v1ilThyBati12019-12-1732266_6#3220,410,86633,282,040,766SAMEA7519961ERR6003047qc completeThyatira batis (1.00)
Hi-C - Arima v1ilThyBati12019-12-1732266_4#3231,745,68034,993,597,680SAMEA7519961ERR6003046qc completeThyatira batis (1.00)
Hi-C - Arima v1ilThyBati12019-12-1732266_5#3226,415,80634,188,786,706SAMEA7519961ERR6002752qc completeThyatira batis (1.00)
Chromium genomeilThyBati12019-11-1831782_7#396,514,18814,573,642,388SAMEA7519960ERR6003045qc completeThyatira batis (1.00)
Chromium genomeilThyBati12019-11-1831782_7#280,962,89012,225,396,390SAMEA7519960ERR6002750qc completeThyatira batis (1.00)
Chromium genomeilThyBati12019-11-1831782_7#1109,611,97416,551,408,074SAMEA7519960ERR6002749qc completeThyatira batis (1.00)
Chromium genomeilThyBati12019-11-1831782_7#499,851,17415,077,527,274SAMEA7519960ERR6002751qc completeThyatira batis (1.00)
RNA PolyAilThyBati22021-09-1740838_6#1249,479,5267,471,408,426SAMEA7701595ERR6787419qc completeThyatira batis (1.00)
RNA PolyAilThyBati22022-08-2345657_1#4862,163,6769,386,715,076SAMEA7701594qc completeThyatira batis (1.00)
RNA PolyAilThyBati12021-05-2537935_8#1040,184,5306,067,864,030SAMEA7519960ERR6286710qc completeThyatira batis (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
0.910625NC_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
ilThyBati1

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.purge2020-01-153,107,2092283,308,397214318,692,723C:97.6%[S:96.0%,D:1.6%],F:0.8%,M:1.6%,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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