Tree of Life QC

Info

NCBI taxon id: 3986  NCBI; ENA; GoaT
Order: Malpighiales
Family: Euphorbiaceae
NCBI lineage: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Malpighiales;Euphorbiaceae;Acalyphoideae;Acalypheae;Mercurialis;
GoaT genome size (M): 694 (direct)
GoaT asm span (M): 453 (direct)
GoaT chr no.: 16 (direct)
GoaT haploid no.: 32 (direct)
GoaT ploidy: 6 (direct)
ToLID prefix: ddMerAnnu

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
ddMerAnnu1KDTOL10055ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522242SAMEA7522176
ddMerAnnu1KDTOL10055ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522243SAMEA7522176
ddMerAnnu1KDTOL10055ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522245SAMEA7522176
ddMerAnnu1KDTOL10055ROYAL BOTANIC GARDENS KEWFEMALEFLOWERSAMEA7522240SAMEA7522176
ddMerAnnu1KDTOL10055ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522241SAMEA7522176
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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
pacbioddMerAnnu13128.95506,693,75449.330.5596.740.20
histogram.txt
10xddMerAnnu13189602,996,71458.090.6898.260.38
histogram.txt
hic-arima2ddMerAnnu131-10.00-100.000.00-100.00
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 - HiFiddMerAnnu12021-03-1280537m64178e_210312_150644A01101019,381,087,70315,165SAMEA7522246ERR8705877
PacBio - HiFiddMerAnnu12021-03-1980716m64016e_210319_163411A01101011,872,656,13615,436SAMEA7522246ERR8705876
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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 genomeddMerAnnu12021-04-0637204_2#26140,386,75821,198,400,458SAMEA7522246ERR8702806qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-03-2537020_4#19148,483,93622,421,074,336SAMEA7522241ERR8702803qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-04-0637204_2#28100,638,41015,196,399,910SAMEA7522246ERR8702808qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-03-2537020_4#18183,621,02627,726,774,926SAMEA7522241ERR8702802qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-03-2537020_4#17216,364,72632,671,073,626SAMEA7522241ERR8702801qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-04-0637204_2#25116,722,00417,625,022,604SAMEA7522246ERR8702805qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-04-0637204_2#2787,798,62013,257,591,620SAMEA7522246ERR8702807qc completeMercurialis annua (1.00)
Chromium genomeddMerAnnu12021-03-2537020_4#20102,337,44415,452,954,044SAMEA7522241ERR8702804qc completeMercurialis annua (1.00)
Hi-C - Arima v2ddMerAnnu12021-09-2141009_3#32,840,743,170428,952,218,670SAMEA7522243ERR8702809qc completeMercurialis annua (1.00)
RNA PolyAddMerAnnu12022-08-2345657_1#6842,709,6646,449,159,264SAMEA7522247ERR10123682qc completeMercurialis annua (1.00)
RNA PolyAddMerAnnu12025-05-1350409_7#36104,329,81215,753,801,612SAMEA7522247qc completeMercurialis annua (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
0.932408NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.905377NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.902876[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.902135[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_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
ddMerAnnu1atg000011l1806
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;
ddMerAnnu1atg000024l1806
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;
ddMerAnnu1atg000025l1145
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000026l1142
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000043l1140
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000044l1146
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000054l1146
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000089l1141
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
ddMerAnnu1atg000129l1806
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;
ddMerAnnu1atg000157l1138
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Rickettsiales;Mitochondria;
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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
ddMerAnnu1

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
    ddMerAnnu1hifiasm2021-03-2447,724,9481,325577,395,023C:97.8%[S:94.8%,D:3.0%],F:0.6%,M:1.6%,n:2326-
    ddMerAnnu1hifiasm.purging2021-03-2449,013,522126481,878,087C:97.7%[S:95.2%,D:2.5%],F:0.6%,M:1.7%,n:2326-
    ddMerAnnu1hicanu.purging2021-09-2225,987,460286476,410,720C:97.7%[S:95.5%,D:2.2%],F:0.6%,M:1.7%,n:2326Q51.3-C92.6(10X); Q68.2-C96.1(HiFi)
    ddMerAnnu1hicanu2021-09-2216,629,6091,821721,900,196C:97.8%[S:74.6%,D:23.2%],F:0.6%,M:1.6%,n:2326Q44.9-C94.7(10X); Q67.9-C98.2(HiFi)
    ddMerAnnu1hicanu.purging2021-03-2428,012,827280494,134,146C:97.7%[S:95.4%,D:2.3%],F:0.6%,M:1.7%,n:2326-
    ddMerAnnu1hicanu2021-03-2414,982,6641,990725,585,053C:97.8%[S:74.2%,D:23.6%],F:0.6%,M:1.6%,n:2326-
    ddMerAnnu1hicanu.purging2021-03-1523,164,343307482,711,027C:97.8%[S:95.5%,D:2.3%],F:0.7%,M:1.5%,n:2326-
    ddMerAnnu1hicanu2021-03-1514,387,8661,984720,382,815C:98.0%[S:74.2%,D:23.8%],F:0.6%,M:1.4%,n:2326-
    ddMerAnnu1hifiasm2021-03-1532,363,613989560,004,365C:98.0%[S:94.0%,D:4.0%],F:0.6%,M:1.4%,n:2326-
    ddMerAnnu1hifiasm.purging2021-03-1534,195,928122462,186,609C:98.0%[S:94.7%,D:3.3%],F:0.6%,M:1.4%,n:2326-
    ddMerAnnu1hifiasm2021-09-2231,577,4911,227578,804,774C:97.7%[S:95.5%,D:2.2%],F:0.6%,M:1.7%,n:2326Q48.3-C94.7(10X); Q59.3-C98.2(HiFi)
    ddMerAnnu1hifiasm.purging2021-09-2235,553,674102457,815,424C:97.7%[S:95.6%,D:2.1%],F:0.6%,M:1.7%,n:2326Q52.8-C91.6(10X); Q63.5-C95.2(HiFi)
    ddMerAnnu1hifiasm.1-polished.salsa2021-09-2235,553,45210440,726,36495457,815,696-
    ddMerAnnu1hifiasm.scaff.yahs2021-09-2235,553,45210460,560,39885457,815,004-
    ddMerAnnu1hifiasm.scaff.salsa2021-09-2235,553,45210440,726,36695457,815,704-

    Organelles

    In-progress organelle results from MitoHiFi or Oatk.

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

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