Tree of Life QC

Info

NCBI taxon id: 1918144  NCBI; ENA; GoaT
Order: Diptera
Family: Tachinidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Oestroidea;Tachinidae;Phasiinae;Phasiini;Phasia;
GoaT genome size (M): 691 (ancestor)
GoaT asm span (M): 876 (direct)
GoaT chr no.: 12 (ancestor)
GoaT haploid no.: 6 (ancestor)
GoaT ploidy: 3 (ancestor)
ToLID prefix: idPhaObes

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
idPhaObes1Ox000770UNIVERSITY OF OXFORDNOT_COLLECTEDWHOLE_ORGANISMSAMEA7746583SAMEA7746483
idPhaObes2Ox001761UNIVERSITY OF OXFORDMALEWHOLE_ORGANISMSAMEA10979409SAMEA10979021
idPhaObes3NHMUK013805878NATURAL HISTORY MUSEUMNOT_PROVIDEDABDOMENSAMEA111458359SAMEA111458040
idPhaObes3NHMUK013805878NATURAL HISTORY MUSEUMNOT_PROVIDEDHEADSAMEA111458217SAMEA111458040
idPhaObes3NHMUK013805878NATURAL HISTORY MUSEUMNOT_PROVIDEDTHORAXSAMEA111458126SAMEA111458040
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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
10xidPhaObes13123.2875,720,14846.992.0698.450.49
histogram.txt
pacbioidPhaObes13115.88749,948,24838.682.0397.890.22
histogram.txt
hic-arima2idPhaObes23150.63901,498,804163.6444.2797.200.35
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 - HiFiidPhaObes12021-04-0381044m64230e_210403_120226C0110214,622,954,64316,205SAMEA7746583ERR10355973
PacBio - HiFi (ULI)idPhaObes12022-09-13TRACTION-RUN-249m64174e_220913_041213D01102220,992,122,8098,785SAMEA7746583ERR10355972
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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
Chromium genomeidPhaObes12021-06-0137642_3#35108,919,59216,446,858,392SAMEA7746583ERR10297873qc completePhasia obesa (1.00)
Chromium genomeidPhaObes12021-06-0137642_3#33152,821,00423,075,971,604SAMEA7746583ERR10297871qc completePhasia obesa (1.00)
Chromium genomeidPhaObes12021-06-0137642_3#3494,993,37214,343,999,172SAMEA7746583ERR10297872qc completePhasia obesa (1.00)
Chromium genomeidPhaObes12021-06-0137642_3#3674,574,88211,260,807,182SAMEA7746583ERR10297874qc completePhasia obesa (1.00)
Hi-C - Arima v2idPhaObes22022-09-2145846_1#4840,144,286126,861,787,186SAMEA10979409ERR10297875qc completePhasia obesa (1.00)
RNA PolyAidPhaObes32024-03-1548593_1#563,798,1369,633,518,536SAMEA111458126qc complete
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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
0.989958[120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...]
0.986519NC_021089.1 Wolbachia endosymbiont of Drosophila simulans wHa, complete genome
0.943219NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.913621[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.91124[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.909369[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.909049[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.908727NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.903242[130 seqs] NZ_MUJL01000001.1 Wolbachia pipientis wUni gwu.contig.0_1, whole genome shotgun sequence [...]
0.902876[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 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
idPhaObes1atg003530l1937
  • 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;
idPhaObes1atg004940l2000
  • 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;
idPhaObes1atg005631l1976
  • 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;
idPhaObes1ptg000129l1499
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
idPhaObes1ptg000257l1982
  • 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;
idPhaObes1ptg001174l1500
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
idPhaObes1ptg001709l792
  • 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;
idPhaObes1ptg002115l963
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Diptera;Brachycera;Muscomorpha;Oestroidea;Tachinidae;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Diptera;
idPhaObes1ptg004726l1987
  • 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;
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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
idPhaObes1Anaplasmataceae10,6330.4C:100.0%[S:0.0%,D:100.0%],F:0.0%,M:0.0%,n:364C:99.7%[S:1.1%,D:98.6%],F:0.0%,M:0.3%,n:36442.59Mb10,030C:99.7%[S:0.5%,D:99.2%],F:0.0%,M:0.3%,n:36422.61Mb
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Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.

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specimen
visualisation
idPhaObes1

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

  • idPhaObes1.hifiasm.20220921

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
idPhaObes1hifiasm2022-09-21424,2485,0121,037,074,116C:98.9%[S:84.0%,D:14.9%],F:0.1%,M:1.0%,n:1367Q46.0-C95.5(10X); Q55.4-C98.9(HiFi)
idPhaObes1hifiasm.purging2022-09-21496,9493,288884,314,648C:98.8%[S:97.1%,D:1.7%],F:0.1%,M:1.1%,n:1367Q46.3-C94.8(10X); Q55.4-C98.3(HiFi)
idPhaObes1hifiasm.scaffolding.salsa2022-09-21491,7033,30310,025,5221,246885,343,148C:99.0%[S:97.5%,D:1.5%],F:0.1%,M:0.9%,n:1367Q46.3-C94.8(10X); Q55.4-C98.3(HiFi)
idPhaObes1hifiasm.scaffolding.yahs2022-09-21472,8473,401146,845,135794884,836,048C:99.0%[S:97.5%,D:1.5%],F:0.1%,M:0.9%,n:1367Q46.3-C94.8(10X); Q55.4-C98.3(HiFi)
idPhaObes1hicanu.purging2022-09-21277,1955,923901,325,703C:98.6%[S:95.2%,D:3.4%],F:0.5%,M:0.9%,n:1367Q47.0-C95.4(10X); Q64.2-C98.9(HiFi)
idPhaObes1hicanu2022-09-21212,28715,7441,773,699,292C:99.3%[S:6.9%,D:92.4%],F:0.3%,M:0.4%,n:1367Q45.8-C99.8(10X); Q64.8-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
seqs
reference
idPhaObes1mitohifi.hifiasmmito2022-09-2117,45937NoneTrue1MK644821.1; 15,792 bp; 37 genes
idPhaObes1mitohifi.hicanumito2022-09-2113,53134COX3False1MK644821.1; 15,792 bp; 37 genes
idPhaObes1mitohifi.readsmito2022-09-2117,45937NoneFalse1MK644821.1; 15,792 bp; 37 genes
WTSI

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