Tree of Life QC

Info

NCBI taxon id: 988148  NCBI; ENA; GoaT
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Noctuinae;Apameini;Photedes;
GoaT genome size (M): 650 (ancestor)
GoaT asm span (M): 617 (ancestor)
GoaT chr no.: 58 (ancestor)
GoaT haploid no.: 29 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: ilPhoMini

Specimens

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

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tolid
specimen_id
gal
sex
organism_part
biosample
biospecimen
ilPhoMini1Ox000672UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7701719SAMEA7701533
ilPhoMini2Ox003713UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA114645394SAMEA114644765
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Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

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source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
pacbioilPhoMini13129.91683,689,90539.570.6497.760.19
histogram.txt
hic-arima2ilPhoMini23191.17513,801,3690.00100.001.110.21
histogram.txt

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 - HiFiilPhoMini12021-02-0879650m64174e_210208_130019D01101616,615,540,92414,693SAMEA7701719ERR12370428
PacBio - HiFiilPhoMini12021-03-1480540m64089e_210314_025301B01101626,862,002,25516,833SAMEA7701719ERR12370427
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ONT run data

Below are stats for each ONT seqeuncing run collected for this species.

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pipeline
specimen
date
run id
flowcell
type
yield
N50
sample accession
report
No matching records found

Illumina run data

Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.

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pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
Hi-C - Arima v2ilPhoMini22024-09-1649524_2#9833,270,980125,823,917,980SAMEA114645394ERR13702755qc completePhotedes minima (1.00)
RNA PolyAilPhoMini22024-11-1949828_8#1691,498,46613,816,268,366SAMEA114645394qc completePhotedes minima (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
0.916705[23 seqs] NZ_JRXV01000021.1 Pseudomonas fluorescens strain AU10973 Contig_17, whole genome shotgun sequence [...]
0.915049NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.91391[608 seqs] NZ_MAYS01000001.1 Candidatus Erwinia dacicola strain IL contig_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
ilPhoMini1atg000420l1547
  • ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;
ilPhoMini1ptg000020l1898
  • 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;
ilPhoMini1ptg000053l1538
  • ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;
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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
ilPhoMini1

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

  • ilPhoMini1.hifiasm.20240916

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
ilPhoMini1hifiasm.purging2024-09-1624,299,19479703,578,360C:99.4%[S:98.8%,D:0.6%],F:0.2%,M:0.4%,n:1367Q66.8-C98.7(HiFi)
ilPhoMini1hifiasm2024-09-1624,299,194183710,264,194C:99.4%[S:98.8%,D:0.6%],F:0.2%,M:0.4%,n:1367Q64.8-C98.7(HiFi)
ilPhoMini1hifiasm.scaffolding.yahs2024-09-1624,175,5478424,269,33979703,579,360C:99.4%[S:98.9%,D:0.5%],F:0.2%,M:0.4%,n:1367Q66.8-C98.7(HiFi)
ilPhoMini1hifiasm.scaffolding_alt.yahs2024-09-162,340,1821,06623,326,503578695,530,964C:98.6%[S:97.9%,D:0.7%],F:0.5%,M:0.9%,n:1367Q64.8-C98.7(HiFi)
ilPhoMini1hicanu.purging2021-03-179,458,071276701,022,223C:99.2%[S:98.6%,D:0.6%],F:0.3%,M:0.5%,n:1367-
ilPhoMini1hicanu2021-03-173,019,1062,5371,432,613,988C:99.5%[S:70.6%,D:28.9%],F:0.2%,M:0.3%,n:1367-
ilPhoMini1hifiasm.purging2021-03-1724,045,795119696,543,298C:99.3%[S:99.0%,D:0.3%],F:0.2%,M:0.5%,n:1367-
ilPhoMini1hifiasm2021-03-1724,045,795209704,619,445C:99.3%[S:98.9%,D:0.4%],F:0.2%,M:0.5%,n:1367-
ilPhoMini1hicanu.purging2022-10-306,423,874361702,829,738C:99.2%[S:98.5%,D:0.7%],F:0.2%,M:0.6%,n:1367Q70.6-C98.7(HiFi)
ilPhoMini1hicanu2022-10-302,579,2922,9241,444,801,967C:99.3%[S:1.8%,D:97.5%],F:0.2%,M:0.5%,n:1367Q69.7-C100.0(HiFi)
ilPhoMini1hifiasm.purging2022-10-3023,811,131111698,754,924C:99.3%[S:99.0%,D:0.3%],F:0.2%,M:0.5%,n:1367Q68.3-C98.7(HiFi)
ilPhoMini1hifiasm2022-10-3023,811,131194714,783,160C:99.5%[S:96.9%,D:2.6%],F:0.2%,M:0.3%,n:1367Q66.8-C98.7(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
seqs
reference
ilPhoMini1mitohifi.readsmito2024-09-1615,38137NoneTrue1NC_086844.1; 15,447 bp; 37 genes
ilPhoMini1mitohifi.hifiasmmito2024-09-1615,38337NoneTrue1NC_086844.1; 15,447 bp; 37 genes
ilPhoMini1mitohifi.readsmito2022-10-3015,38637NoneTrue1NC_065464.1; 15,409 bp; 37 genes
ilPhoMini1mitohifi.hicanumito2022-10-3015,38137NoneTrue1NC_065464.1; 15,409 bp; 37 genes
ilPhoMini1mitohifi.hifiasmmito2022-10-3015,38537NoneTrue1NC_065464.1; 15,409 bp; 37 genes
WTSI

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