Tree of Life QC

Info

NCBI taxon id: 1126402  NCBI; ENA; GoaT
Order: Hymenoptera
Family: Andrenidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Hymenoptera;Apocrita;Aculeata;Apoidea;Anthophila;Andrenidae;Andreninae;Andrena;
GoaT genome size (M): 489 (ancestor)
GoaT asm span (M): 428 (direct)
GoaT chr no.: 6 (ancestor)
GoaT haploid no.: 3 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: iyAndHatt

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
iyAndHatt1Ox000755UNIVERSITY OF OXFORDFEMALEABDOMENSAMEA7746552SAMEA7746468
iyAndHatt1Ox000755UNIVERSITY OF OXFORDFEMALEHEADSAMEA7746550SAMEA7746468
iyAndHatt1Ox000755UNIVERSITY OF OXFORDFEMALETHORAXSAMEA7746551SAMEA7746468
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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
pacbioiyAndHatt13124.59443,761,10240.040.1396.690.20
histogram.txt
hic-arima2iyAndHatt13176.69648,069,33059.770.6698.100.34
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 - HiFiiyAndHatt12021-03-2280705m64230e_210322_134758D01100823,269,138,12315,827SAMEA7746551ERR9630942
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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
Hi-C - Arima v2iyAndHatt12021-03-2236943_4#4904,459,270136,573,349,770SAMEA7746550ERR9580473qc completeAndrena hattorfiana (1.00)
RNA PolyAiyAndHatt12022-08-2345657_1#6967,097,36210,131,701,662SAMEA7746552ERR10123693qc completeAndrena hattorfiana (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
0.963897[157 seqs] NZ_LSYX01000001.1 Wolbachia endosymbiont of Dactylopius coccus strain wDacA Contig_1, whole genome shotgun sequence [...]
0.925557[256 seqs] NZ_ACFP01000256.1 Wolbachia endosymbiont of Muscidifurax uniraptor Contig561, whole genome shotgun sequence [...]
0.915049NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.900227[182 seqs] NZ_LYUV01000001.1 Wolbachia endosymbiont of Nomada leucophthalma strain wNleu NODE_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
iyAndHatt1atg000349l1922
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1atg000863l1927
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1ptg000002l1920
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1ptg000037l1921
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1ptg000099l1894
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1ptg000115l1272
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Hymenoptera;Apocrita;Aculeata;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Hymenoptera;
iyAndHatt1ptg000258l1499
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachieae;Wolbachia;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Anaplasmataceae;Wolbachia;
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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
iyAndHatt1Anaplasmataceae7600.05C:93.4%[S:10.2%,D:83.2%],F:4.4%,M:2.2%,n:364C:89.0%[S:89.0%,D:0.0%],F:2.2%,M:8.8%,n:36461.31Mb690C:89.0%[S:89.0%,D:0.0%],F:3.0%,M:8.0%,n:36441.34Mb11
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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
iyAndHatt1

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

  • iyAndHatt1.hifiasm.20220207

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
iyAndHatt1hifiasm2022-02-219,991,7981,300483,113,046-
iyAndHatt1hifiasm.purging2022-02-0711,278,044303429,956,666C:98.7%[S:98.5%,D:0.2%],F:0.1%,M:1.2%,n:1367Q64.2-C98.1(HiFi)
iyAndHatt1hifiasm2022-02-0710,245,246855465,097,738C:99.2%[S:99.0%,D:0.2%],F:0.1%,M:0.7%,n:1367Q60.0-C98.4(HiFi)
iyAndHatt1hifiasm.scaffolding.salsa2022-02-0710,514,16332017,007,066279429,977,166C:98.8%[S:98.6%,D:0.2%],F:0.1%,M:1.1%,n:1367Q64.2-C98.1(HiFi)
iyAndHatt1hifiasm.scaffolding.yahs2022-02-0710,245,24634226,739,052280429,969,066C:98.7%[S:98.5%,D:0.2%],F:0.1%,M:1.2%,n:1367Q64.2-C98.1(HiFi)
iyAndHatt1hicanu2022-02-073,575,8003,210563,650,046C:99.3%[S:80.5%,D:18.8%],F:0.1%,M:0.6%,n:1367Q65.4-C98.7(HiFi)
iyAndHatt1hicanu.purging2022-02-079,991,539912438,986,792C:98.7%[S:98.5%,D:0.2%],F:0.1%,M:1.2%,n:1367Q66.2-C98.3(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
iyAndHatt1mitohifi.hifiasmmito2022-02-0745,8576NoneNC_042768.1; 15,804 bp; 37 genes
iyAndHatt1mitohifi.hifiasmmito2022-02-0715,23532NoneTrueEU302588.1; 16,953 bp; 41 genes
iyAndHatt1mitohifi.hifiasmmito2022-02-0715,23537NoneTrueNC_062184.1; 15,239 bp; 37 genes
iyAndHatt1mitohifi.hicanumito2022-02-0764,4989NoneNC_042768.1; 15,804 bp; 37 genes
iyAndHatt1mitohifi.readsmito2022-02-0758,2878NoneFalseNC_061380.1; 16,447 bp; 37 genes
iyAndHatt1mitohifi.readsmito2022-02-0716,31732NoneFalseNC_042768.1; 15,804 bp; 37 genes
iyAndHatt1mitohifi.readsmito2022-02-0722,74936NoneNC_042768.1; 15,804 bp; 37 genes
WTSI

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