Tree of Life QC

Info

NCBI taxon id: 1101110
Order: Lepidoptera
Family: Pyralidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Pyraloidea;Pyralidae;Pyralinae;Hypsopygia;
GoaT genome size (M): 601 (ancestor)
GoaT asm span (M): 816 (direct)
GoaT chr no.: 60 (ancestor)
ToLID prefix: ilHypCost

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
ilHypCost1Ox000559UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7701424SAMEA7701325
ilHypCost2Ox000560UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA8603376SAMEA8603124
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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-arima2ilHypCost23146.3821,069,8730.00100.001.670.26
10xilHypCost13119.07877,881,17744.831.8299.510.39
pacbioilHypCost13124.13787,935,51937.411.7798.480.14

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 - HiFiilHypCost12021-05-0381871m64221e_210503_104409D01100819,313,142,24513,790SAMEA7701424ERR9127941
PacBio - HiFi (ULI)ilHypCost12022-02-12TRACTION-RUN-72m64178e_220212_222137B01-20,464,682,71010,042SAMEA7701424ERR9468770
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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 v2ilHypCost22021-05-2738173_4#3676,894,778102,211,111,478SAMEA8603376ERR9123822qc completeHypsopygia costalis (1.00)
Chromium genomeilHypCost12021-06-0137642_2#1873,587,71011,111,744,210SAMEA7701424ERR9123819qc completeHypsopygia costalis (1.00)
Chromium genomeilHypCost12021-06-0137642_2#1780,345,93612,132,236,336SAMEA7701424ERR9123818qc completeHypsopygia costalis (1.00)
Chromium genomeilHypCost12021-06-0137642_2#2090,530,61213,670,122,412SAMEA7701424ERR9123821qc completeHypsopygia costalis (1.00)
Chromium genomeilHypCost12021-06-0137642_2#19100,442,84215,166,869,142SAMEA7701424ERR9123820qc completeHypsopygia costalis (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
0.923264NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.906067[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.903242NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, 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
ilHypCost1atg001049l626
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilHypCost1ptg000036l1900
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
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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
ilHypCost1

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

  • ilHypCost1.hifiasm.20220815

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
ilHypCost1hicanu2022-08-151,978,1914,9791,680,766,509C:99.2%[S:5.4%,D:93.8%],F:0.3%,M:0.5%,n:1367Q43.4-C99.7(10X); Q66.6-C100.0(HiFi)
ilHypCost1hicanu.purging2022-08-153,739,273511826,511,745C:99.1%[S:97.1%,D:2.0%],F:0.3%,M:0.6%,n:1367Q48.5-C97.1(10X); Q67.3-C99.1(HiFi)
ilHypCost1hifiasm2022-02-1923,969,310147838,604,491C:99.1%[S:96.5%,D:2.6%],F:0.3%,M:0.6%,n:1367Q49.1-C97.1(10X); Q64.4-C99.1(HiFi)
ilHypCost1hifiasm.polishing_2022-02-1923,969,14963819,614,325C:99.0%[S:98.3%,D:0.7%],F:0.3%,M:0.7%,n:1367Q49.6-C97.1(10X); Q58.3-C99.1(HiFi)
ilHypCost1hifiasm.purging2022-02-1923,969,31063819,620,824C:99.0%[S:98.3%,D:0.7%],F:0.3%,M:0.7%,n:1367Q49.1-C97.1(10X); Q64.8-C99.1(HiFi)
ilHypCost1hifiasm.scaff.salsa2022-02-1920,575,0126728,835,48446819,631,324-
ilHypCost1hifiasm.scaff.yahs2022-02-1920,575,0127428,835,18447819,626,224-
ilHypCost1hifiasm.scaffolding.salsa2022-02-1920,574,8956728,835,23046819,624,825C:99.0%[S:98.2%,D:0.8%],F:0.3%,M:0.7%,n:1367Q49.6-C97.1(10X); Q58.3-C99.1(HiFi)
ilHypCost1hifiasm.scaffolding.yahs2022-02-1920,574,8957328,834,93046819,619,725C:99.1%[S:98.2%,D:0.9%],F:0.3%,M:0.6%,n:1367Q49.6-C97.1(10X); Q58.3-C99.1(HiFi)
ilHypCost1hicanu2022-02-191,748,8643,7911,653,677,739C:99.2%[S:5.6%,D:93.6%],F:0.4%,M:0.4%,n:1367Q44.1-C97.1(10X); Q67.2-C99.2(HiFi)
ilHypCost1hicanu.purging2022-02-193,051,428590828,500,807C:98.9%[S:96.6%,D:2.3%],F:0.4%,M:0.7%,n:1367Q48.2-C97.1(10X); Q67.3-C99.1(HiFi)
ilHypCost1hifiasm2022-08-1526,656,789163831,808,010C:99.0%[S:97.1%,D:1.9%],F:0.3%,M:0.7%,n:1367Q49.3-C97.1(10X); Q65.3-C99.1(HiFi)
ilHypCost1hifiasm.purging2022-08-1526,785,87965819,640,719C:99.0%[S:98.4%,D:0.6%],F:0.3%,M:0.7%,n:1367Q49.4-C97.1(10X); Q65.6-C99.1(HiFi)
ilHypCost1hifiasm.scaffolding.salsa2022-08-1526,785,8797029,066,42053819,649,219C:99.0%[S:98.3%,D:0.7%],F:0.3%,M:0.7%,n:1367Q49.4-C97.1(10X); Q65.6-C99.1(HiFi)
ilHypCost1hifiasm.scaffolding.yahs2022-08-1526,785,8797828,887,35853819,645,719C:99.0%[S:98.4%,D:0.6%],F:0.3%,M:0.7%,n:1367Q49.4-C97.1(10X); Q65.6-C99.1(HiFi)

Organelles

In-progress organelle results from MitoHiFi2.

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specimen
asm
date
length
genes
frameshifts
is circular
reference
ilHypCost1hicanu2022-08-1515,27037NoneTrueNC_030508.1; 15,212 bp; 37 genes
ilHypCost1hifiasm2022-02-1915,27937COX1;COX2NC_030508.1; 15,212 bp; 37 genes
ilHypCost1hicanu2022-02-1915,27037NoneNC_030508.1; 15,212 bp; 37 genes
ilHypCost1reads2022-02-1920,81537ND5NC_030508.1; 15,212 bp; 37 genes
ilHypCost1hifiasm2022-08-1515,27737NoneTrueNC_030508.1; 15,212 bp; 37 genes
WTSI

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