Tree of Life QC

Info

NCBI taxon id: 1219160  NCBI; ENA; GoaT
Order: Diptera
Family: Conopidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Conopoidea;Conopidae;Conopinae;Physocephala;
GoaT genome size (M): 260 (ancestor)
GoaT asm span (M): 210 (ancestor)
GoaT chr no.: 12 (ancestor)
GoaT haploid no.: 4 (ancestor)
GoaT ploidy: 3 (ancestor)
ToLID prefix: idPhyRufi

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
idPhyRufi1Ox000756UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7746555SAMEA7746469
idPhyRufi1Ox000756UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7746554SAMEA7746469
idPhyRufi1Ox000756UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA7746553SAMEA7746469
idPhyRufi2Ox001854UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA10979517SAMEA10979113
idPhyRufi2Ox001854UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA10979519SAMEA10979113
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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
illuminaidPhyRufi33130.1304,356,40736.701.3898.450.17
10xidPhyRufi13133.34605,592,30369.081.5298.930.42
pacbioidPhyRufi13122.89231,293,08128.771.7297.640.20
hic-arima2idPhyRufi131237.5206,711,53141.7823.5898.520.45
illuminaidPhyRufi23128.41286,789,38532.781.3498.130.15
illuminaidPhyRufi43132.52299,650,42935.791.4098.300.15

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 - HiFiidPhyRufi12021-05-2482553m64094e_210524_093354D01101911,307,230,21213,167SAMEA7746554ERR9854838
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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
StandardidPhyRufi32024-01-2648341_1#7159,822,82624,133,246,726SAMEA112222071qc completePhysocephala rufipes (1.00)
Chromium genomeidPhyRufi12021-06-1638403_2#44131,743,87419,893,324,974SAMEA7746554qc completePhysocephala rufipes (1.00)
Chromium genomeidPhyRufi12021-06-1638403_2#4186,212,77413,018,128,874SAMEA7746554qc completePhysocephala rufipes (1.00)
Chromium genomeidPhyRufi12021-06-1638403_2#43113,731,08217,173,393,382SAMEA7746554qc completePhysocephala rufipes (1.00)
Chromium genomeidPhyRufi12021-06-1638403_2#4287,862,61613,267,255,016SAMEA7746554qc completePhysocephala rufipes (1.00)
Hi-C - Arima v2idPhyRufi12021-05-2738173_1#1922,988,162139,371,212,462SAMEA7746553ERR9866450qc completePhysocephala rufipes (1.00)
StandardidPhyRufi22024-01-2648341_1#5141,220,28621,324,263,186SAMEA10979518qc completePhysocephala rufipes (1.00)
StandardidPhyRufi42024-01-2648341_1#6168,816,73825,491,327,438SAMEA112221937qc completePhysocephala rufipes (1.00)
RNA PolyAidPhyRufi12022-09-2945898_4#1573,705,75811,129,569,458SAMEA7746555ERR10378017qc completePhysocephala rufipes (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
0.926002NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, 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
idPhyRufi1atg000467l1990
  • 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;
idPhyRufi1atg002982l866
  • ENA: Eukaryota;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;
idPhyRufi1ptg000031l1977
  • 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;
idPhyRufi1ptg000492l1422
  • 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;
idPhyRufi1ptg000700l1277
  • 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;
idPhyRufi1ptg000888l1987
  • 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;
idPhyRufi1ptg001530l1808
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;
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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
idPhyRufi1

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

  • idPhyRufi1.hifiasm.20220613

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
idPhyRufi1hifiasm-hic2022-06-13767,4311,632263,055,387C:95.0%[S:91.3%,D:3.7%],F:0.4%,M:4.6%,n:1367Q44.6-C88.2(10X); Q52.9-C98.5(HiFi)
idPhyRufi1hifiasm2022-06-13767,4311,597262,671,170C:95.0%[S:91.7%,D:3.3%],F:0.4%,M:4.6%,n:1367Q44.5-C88.2(10X); Q52.5-C98.5(HiFi)
idPhyRufi1hifiasm.purging2022-06-13830,6931,307243,716,660C:95.0%[S:94.0%,D:1.0%],F:0.4%,M:4.6%,n:1367Q44.6-C87.6(10X); Q52.6-C97.9(HiFi)
idPhyRufi1hifiasm.scaff.yahs2022-06-13768,0431,39530,229,860585243,878,660-
idPhyRufi1hifiasm.scaff.yahs2022-06-13768,0431,39530,237,840842243,827,260-
idPhyRufi1hifiasm.polishing2022-06-13830,6901,307243,714,187C:95.0%[S:94.0%,D:1.0%],F:0.4%,M:4.6%,n:1367Q45.3-C87.7(10X); Q49.8-C98.0(HiFi)
idPhyRufi1hifiasm.scaffolding.salsa2022-06-13816,9291,3189,248,067724244,011,187C:94.9%[S:93.9%,D:1.0%],F:0.4%,M:4.7%,n:1367Q45.3-C87.7(10X); Q49.8-C98.0(HiFi)
idPhyRufi1hifiasm.scaffolding.yahs2022-06-13768,0141,39343,036,968650243,862,787-
idPhyRufi1hifiasm.scaffolding.yahs2022-06-13768,0141,39323,845,358868243,819,187C:94.9%[S:93.9%,D:1.0%],F:0.5%,M:4.6%,n:1367Q45.3-C87.7(10X); Q49.8-C98.0(HiFi)
idPhyRufi1hicanu.purging2022-06-13455,9842,226259,508,228C:95.8%[S:94.2%,D:1.6%],F:0.5%,M:3.7%,n:1367Q44.4-C88.6(10X); Q63.8-C98.8(HiFi)
idPhyRufi1hicanu2022-06-13339,6735,162508,976,259C:96.3%[S:4.9%,D:91.4%],F:0.5%,M:3.2%,n:1367Q43.1-C99.8(10X); Q63.9-C100.0(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
idPhyRufi1mitohifi.hifiasmmito2022-06-1322,34437NoneTrueNC_063616.1; 17,125 bp; 37 genes
idPhyRufi1mitohifi.hicanumito2022-06-1321,02337NoneTrueNC_063616.1; 17,125 bp; 37 genes
idPhyRufi1mitohifi.readsmito2022-06-1318,22237NoneTrueNC_063616.1; 17,125 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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