Tree of Life QC

Info

NCBI taxon id: 219539
Order: Diptera
Family: Syrphidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Syrphinae;Syrphini;Scaeva;
GoaT genome size (M): 528 (ancestor)
GoaT asm span (M): 320 (direct)
GoaT chr no.: 8 (direct)
ToLID prefix: idScaPyra

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
idScaPyra1Ox000142UNIVERSITY OF OXFORDFEMALEABDOMENSAMEA7520227SAMEA7520160
idScaPyra1Ox000142UNIVERSITY OF OXFORDFEMALETHORAXSAMEA7520226SAMEA7520160
idScaPyra1Ox000142UNIVERSITY OF OXFORDFEMALEHEADSAMEA7520226SAMEA7520160
idScaPyra2NHMUK014111090NATURAL HISTORY MUSEUMMALEHEADSAMEA7521604SAMEA7521523
idScaPyra2NHMUK014111090NATURAL HISTORY MUSEUMMALETHORAXSAMEA7521605SAMEA7521523
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1025
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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
10xidScaPyra13160.65334,736,02126.842.1092.560.48
pacbioidScaPyra13160.98300,391,93714.112.0590.400.26
hic-arima2idScaPyra13153.79417,897,3570.00100.004.160.34

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 - HiFiidScaPyra12019-11-3073397m64089_191130_132500B01102010,124,760,83815,327SAMEA7520226ERR7057609
PacBio - HiFiidScaPyra12020-02-2275230m64094_200222_164026C01102129,675,929,74414,227SAMEA7520226ERR7057610
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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 genomeidScaPyra12020-02-2433254_1#3121,285,51618,314,112,916SAMEA7520226ERR6787406qc completeScaeva pyrastri (1.00)
Chromium genomeidScaPyra12020-02-2433254_1#447,640,7607,193,754,760SAMEA7520226ERR6787407qc completeScaeva pyrastri (1.00)
Chromium genomeidScaPyra12020-02-2433254_1#2147,898,55822,332,682,258SAMEA7520226ERR6787405qc completeScaeva pyrastri (1.00)
Chromium genomeidScaPyra12020-02-2433254_1#1112,256,85416,950,784,954SAMEA7520226ERR6787404qc completeScaeva pyrastri (1.00)
Hi-C - Arima v2idScaPyra12020-08-2834892_7#3135,036,92620,390,575,826SAMEA7520227ERR6787409qc completeScaeva pyrastri (1.00)
Hi-C - Arima v2idScaPyra12020-08-2834892_8#3136,847,62820,663,991,828SAMEA7520227ERR6787410qc completeScaeva pyrastri (1.00)
Hi-C - Arima v2idScaPyra12020-08-2834892_6#3140,121,02221,158,274,322SAMEA7520227ERR6787408qc completeScaeva pyrastri (1.00)
RNA PolyAidScaPyra22021-05-2537935_6#943,494,2486,567,631,448SAMEA7521605ERR6787411qc completeScaeva pyrastri (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
0.934114NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.909049[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.906409[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.903965[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
0.902135[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.900227NZ_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
idScaPyra1

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
    idScaPyra1hicanu2020-10-176,217,4661,222659,104,130C:98.8%[S:3.9%,D:94.9%],F:0.5%,M:0.7%,n:1658-
    idScaPyra1hicanu.purging2020-10-176,445,270406326,851,222C:98.5%[S:98.3%,D:0.2%],F:0.8%,M:0.7%,n:1658-
    idScaPyra1hifiasm2020-10-178,616,130258328,301,799C:98.5%[S:97.1%,D:1.4%],F:0.8%,M:0.7%,n:1658-
    idScaPyra1hifiasm.purging2020-10-178,651,711182322,601,873C:98.4%[S:97.6%,D:0.8%],F:0.8%,M:0.8%,n:1658-
    idScaPyra1hifiasm.scaffolding.salsa2020-10-178,651,64118424,852,08497322,643,433-
    idScaPyra1hifiasm.scaffolding2020-10-178,651,64118224,852,08495322,643,433-

    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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