Tree of Life QC

Info

NCBI taxon id: 226145
Order: Diptera
Family: Syrphidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Eristalinae;Rhingiini;Ferdinandea;
GoaT genome size (M): 528 (ancestor)
GoaT asm span (M): 684 (ancestor)
GoaT chr no.: 10 (ancestor)
GoaT ploidy: 3 (ancestor)
ToLID prefix: idFerCupr

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
idFerCupr1Ox000108UNIVERSITY OF OXFORDFEMALETHORAXSAMEA7520141SAMEA7520047
idFerCupr1Ox000108UNIVERSITY OF OXFORDFEMALEHEADSAMEA7520141SAMEA7520047
idFerCupr1Ox000108UNIVERSITY OF OXFORDFEMALEABDOMENSAMEA7520142SAMEA7520047
idFerCupr2NHMUK014444626NATURAL HISTORY MUSEUMNOT_COLLECTEDABDOMENSAMEA7849450SAMEA7849388
idFerCupr2NHMUK014444626NATURAL HISTORY MUSEUMNOT_COLLECTEDHEADSAMEA7849448SAMEA7849388
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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
pacbioidFerCupr23123.53562,764,92427.991.0698.000.14
hic-arimaidFerCupr13134.89686,761,55145.735.5498.590.40
10xidFerCupr13134.41595,055,72233.311.1197.800.41
pacbioidFerCupr1315.78560,501,02930.201.1399.520.10

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 - HiFiidFerCupr12020-01-16TRACTION-RUN-7m64094_200116_113227A0110016,719,529,6177,378SAMEA7520141
PacBio - HiFiidFerCupr22023-06-24TRACTION-RUN-642m64221e_230624_112122E01209227,734,880,49312,181SAMEA7849449ERR11673229
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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 v1idFerCupr12020-09-0935000_6#2449,244,80267,835,965,102SAMEA7520142ERR11679380qc completeFerdinandea cuprea (1.00)
Chromium genomeidFerCupr12020-02-2833253_7#2107,894,46816,292,064,668SAMEA7520141ERR11679377qc completeFerdinandea cuprea (1.00)
Chromium genomeidFerCupr12020-02-2833253_7#4100,701,88615,205,984,786SAMEA7520141ERR11679379qc completeFerdinandea cuprea (1.00)
Chromium genomeidFerCupr12020-02-2833253_7#3116,270,22817,556,804,428SAMEA7520141ERR11679378qc completeFerdinandea cuprea (1.00)
Chromium genomeidFerCupr12020-02-2833253_7#1100,220,44615,133,287,346SAMEA7520141ERR11679376qc completeFerdinandea cuprea (1.00)
RNA PolyAidFerCupr22023-08-0747706_1#3663,472,4929,584,346,292SAMEA7849450qc completeFerdinandea cuprea (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
0.923264[91 seqs] NZ_JDVA01000001.1 Leuconostoc pseudomesenteroides PS12 contig_001, whole genome shotgun sequence [...]
0.914483NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.901381NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
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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
idFerCupr2atg000164l667
  • ENA: Eukaryota;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;
idFerCupr2atg000705l1967
  • 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;Diptera;
idFerCupr2atg000830l1372
  • 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;Diptera;
idFerCupr2atg000911l1996
  • 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;Diptera;
idFerCupr2atg001187l1378
  • 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;Diptera;
idFerCupr2atg001204l1893
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Diptera;Brachycera;Muscomorpha;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;
idFerCupr2atg001768l1929
  • 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;Diptera;
idFerCupr2ptg000078l654
  • ENA: Eukaryota;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;
idFerCupr2ptg000154l1986
  • 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;Diptera;
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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
idFerCupr1

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

  • idFerCupr2.hifiasm.20230626

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
idFerCupr2hicanu.purging2023-06-264,713,495458567,038,966C:99.1%[S:98.1%,D:1.0%],F:0.1%,M:0.8%,n:1367Q70.5-C99.2(HiFi)
idFerCupr2hicanu2023-06-263,485,3732,8161,181,823,178C:99.1%[S:2.0%,D:97.1%],F:0.1%,M:0.8%,n:1367Q69.8-C100.0(HiFi)
idFerCupr2hifiasm2023-06-268,881,436447592,991,478C:98.9%[S:98.5%,D:0.4%],F:0.1%,M:1.0%,n:1367Q60.2-C99.5(HiFi)
idFerCupr2hifiasm.purging2023-06-269,194,414212560,308,192C:98.9%[S:98.5%,D:0.4%],F:0.1%,M:1.0%,n:1367Q62.3-C99.2(HiFi)
idFerCupr2hifiasm.scaffolding.yahs2023-06-268,439,957235124,775,173101560,334,992C:99.2%[S:98.8%,D:0.4%],F:0.1%,M:0.7%,n:1367Q62.3-C99.2(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
idFerCupr2mitohifi.hicanumito2023-06-2616,00137NoneTrueNC_052907.1; 15,907 bp; 37 genes
idFerCupr2mitohifi.readsmito2023-06-2616,00537NoneTrueNC_052907.1; 15,907 bp; 37 genes
WTSI

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