Tree of Life QC

Info

NCBI taxon id: 414876
Order: Diptera
Family: Syrphidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Syrphinae;Syrphini;Xanthogramma;
GoaT genome size (M): 528 (ancestor)
GoaT asm span (M): 977 (direct)
GoaT chr no.: 10 (direct)
ToLID prefix: idXanPedi

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
idXanPedi1NHMUK014111043NATURAL HISTORY MUSEUMMALETHORAXSAMEA7521039SAMEA7520951
idXanPedi1NHMUK014111043NATURAL HISTORY MUSEUMMALEHEADSAMEA7521038SAMEA7520951
idXanPedi1NHMUK014111043NATURAL HISTORY MUSEUMMALEABDOMENSAMEA7521040SAMEA7520951
idXanPedi2Ox000433UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7520729SAMEA7520654
idXanPedi2Ox000433UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7520728SAMEA7520654
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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
10xidXanPedi13128.481,125,471,10253.731.5298.330.56
pacbioidXanPedi13118968,752,04443.801.3798.710.13
hic-omnicidXanPedi13149.53961,098,93750.472.0398.340.57
hic-arima2idXanPedi13115.661,491,892,85655.070.6996.780.39

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 - HiFiidXanPedi12020-08-0176924m64094_200801_182825C01101213,188,962,60811,257SAMEA7521039ERR6412036
PacBio - HiFiidXanPedi12020-08-2077148m64097_200820_135404A01101223,184,313,34111,685SAMEA7521039ERR7254634
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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
Chromium genomeidXanPedi12021-03-0536550_2#588,299,47213,333,220,272SAMEA7521039ERR6054847qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12020-10-1635192_4#486,782,46013,104,151,460SAMEA7521039ERR6054845qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12020-10-1635192_4#296,997,27014,646,587,770SAMEA7521039ERR6054843qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12021-03-0536550_2#883,284,44612,575,951,346SAMEA7521039ERR6054850qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12020-10-1635192_4#379,306,71611,975,314,116SAMEA7521039ERR6054844qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12021-03-0536550_2#775,725,31811,434,523,018SAMEA7521039ERR6054849qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12020-10-1635192_4#193,797,11014,163,363,610SAMEA7521039ERR6054842qc completeXanthogramma pedissequum (1.00)
Chromium genomeidXanPedi12021-03-0536550_2#691,298,47813,786,070,178SAMEA7521039ERR6054848qc completeXanthogramma pedissequum (1.00)
Hi-C - OmniCidXanPedi12022-09-0145601_1#1938,983,756141,786,547,156SAMEA7521038qc completeXanthogramma pedissequum (1.00)
Hi-C - Arima v2idXanPedi12021-01-0635887_4#3435,907,98865,822,106,188SAMEA7521039ERR6054846qc completeXanthogramma pedissequum (1.00)
RNA PolyAidXanPedi42022-03-2544268_5#1425,873,1883,906,851,388SAMEA7701345ERR9434980qc completeXanthogramma pedissequum (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
0.93558NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.905724[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.903242[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.903242NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.902507[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.900615[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.900615NZ_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
No matching records found

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
idXanPedi1

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

    Assemblies

    In-progress assembly QC.

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    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    idXanPedi1hicanu2020-12-111,744,8777,3332,004,092,657C:97.9%[S:9.9%,D:88.0%],F:0.7%,M:1.4%,n:1658-
    idXanPedi1hicanu.purging_e2020-12-112,683,0791,6732,759,1401,600987,872,049-
    idXanPedi1hicanu.purging2020-12-112,716,5301,598992,887,627C:98.0%[S:94.7%,D:3.3%],F:0.7%,M:1.3%,n:1658-
    idXanPedi1hicanu.scaff.salsa2020-12-112,482,5821,72024,427,2891,168988,102,070-
    idXanPedi1hicanu.purging_222020-12-112,716,5301,610993,538,011-
    idXanPedi1hicanu.repurging2020-12-112,716,5301,594991,464,054-
    idXanPedi1hifiasm.purging_e2020-12-118,269,6918218,609,714794982,850,222-
    idXanPedi1hifiasm.purging2020-12-118,609,714793997,456,887C:98.0%[S:94.5%,D:3.5%],F:0.7%,M:1.3%,n:1658-
    idXanPedi1hifiasm.scaff.salsa2020-12-117,832,69588893,199,131636982,954,757-
    idXanPedi1hifiasm.purging_222020-12-118,609,714799997,899,224-
    idXanPedi1hifiasm.repurging2020-12-118,609,714781995,856,491-
    idXanPedi1hifiasm2020-12-118,269,6911,2311,069,991,414C:98.0%[S:90.2%,D:7.8%],F:0.7%,M:1.3%,n:1658-

    Organelles

    In-progress organelle results from MitoHiFi2.

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    specimen
    asm
    date
    length
    genes
    frameshifts
    is circular
    reference
    No matching records found
    WTSI

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