Tree of Life QC

Info

NCBI taxon id: 1534653  NCBI; ENA; GoaT
Order: Apiales
Family: Apiaceae
NCBI lineage: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae;Smyrnieae;Smyrnium;
GoaT genome size (M): 2,806 (direct)
GoaT asm span (M): 1,520 (ancestor)
GoaT chr no.: 22 (direct)
GoaT haploid no.: 11 (direct)
GoaT ploidy: 2 (direct)
ToLID prefix: drSmyPerf

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
drSmyPerf1KDTOL10161ROYAL BOTANIC GARDENS KEWHERMAPHRODITE_MONOECIOUSLEAFSAMEA9143787SAMEA9143055
drSmyPerf1KDTOL10161ROYAL BOTANIC GARDENS KEWHERMAPHRODITE_MONOECIOUSLEAFSAMEA9143785SAMEA9143055
drSmyPerf1KDTOL10161ROYAL BOTANIC GARDENS KEWHERMAPHRODITE_MONOECIOUSLEAFSAMEA9143782SAMEA9143055
drSmyPerf1KDTOL10161ROYAL BOTANIC GARDENS KEWHERMAPHRODITE_MONOECIOUSBUDSAMEA9143788SAMEA9143055
drSmyPerf1KDTOL10161ROYAL BOTANIC GARDENS KEWHERMAPHRODITE_MONOECIOUSLEAFSAMEA9143781SAMEA9143055
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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
pacbiodrSmyPerf13126.722,629,421,01973.480.6995.940.16
histogram.txt
hic-arima2drSmyPerf13166.583,113,949,1960.00100.001.090.10
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 - HiFidrSmyPerf12021-08-1485529m64089e_210814_175809C01100115,758,967,95111,307SAMEA9143786
PacBio - HiFidrSmyPerf12021-09-0386238m64089e_210903_150152A0110016,525,764,1089,742SAMEA9143786
PacBio - HiFidrSmyPerf12022-01-0689273m64125e_220106_180822A0110178,028,984,11812,457SAMEA9143786
PacBio - HiFidrSmyPerf12022-01-1489389m64222e_220114_094354C01101610,618,733,40710,232SAMEA9143786
PacBio - HiFidrSmyPerf12022-09-30TRACTION-RUN-272m64221e_220930_155110B01102018,580,398,40012,761SAMEA9143784
PacBio - HiFidrSmyPerf12023-01-31TRACTION-RUN-433m64228e_230131_202101B01101923,952,036,42712,247SAMEA9143784
PacBio - HiFidrSmyPerf12023-02-10TRACTION-RUN-439m64125e_230210_023712D01101921,087,598,61612,326SAMEA9143784
PacBio - HiFidrSmyPerf12023-02-26TRACTION-RUN-469m64174e_230226_010448D01101922,263,929,78412,041SAMEA9143784
PacBio - HiFidrSmyPerf12023-06-17TRACTION-RUN-624m64178e_230617_032702D01206021,313,731,82212,013SAMEA9143786
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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 v2drSmyPerf12022-05-1744925_3#23,538,497,948534,313,190,148SAMEA9143784qc completeSmyrnium perfoliatum (1.00)
RNA PolyAdrSmyPerf12023-11-0248017_1#4249,016,1387,401,436,838SAMEA9143784qc completeSmyrnium perfoliatum (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
0.929005NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.903965[104 seqs] NZ_AODN01000001.1 Rhodococcus qingshengii BKS 20-40 Contig001, whole genome shotgun sequence [...]
0.902876[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.902135[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.902135NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.901759[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.901381[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.901381[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.901[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...]
0.901NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
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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
drSmyPerf1atg000099l1361
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drSmyPerf1atg000283l931
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drSmyPerf1atg000577l827
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;Apiaceae;Apioideae;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;Cnidium;
drSmyPerf1atg001286l639
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg004895l637
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg006850l1827
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg006929l1466
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg007176l1814
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg009011l1805
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
drSmyPerf1atg009271l1873
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;asterids;campanulids;Apiales;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Apiales;
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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
drSmyPerf1

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

  • drSmyPerf1.hifiasm.20230216

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
drSmyPerf1hifiasm-hic2023-02-1633,844,7805,5852,698,293,684C:98.5%[S:89.7%,D:8.8%],F:0.4%,M:1.1%,n:2326Q59.0-C97.5(HiFi)
drSmyPerf1hicanu2023-02-165,402,22623,2703,808,665,299C:98.7%[S:51.4%,D:47.3%],F:0.4%,M:0.9%,n:2326Q61.3-C100.0(HiFi)
drSmyPerf1hifiasm2023-02-1634,032,9145,5862,698,011,435C:98.5%[S:89.8%,D:8.7%],F:0.4%,M:1.1%,n:2326Q58.9-C97.4(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
drSmyPerf1oatk.readsmito2023-02-1617,031TrueNC_072550.1; bp; 0 genes
drSmyPerf1oatk.readspltd2023-02-1683,25326NoneFalseNC_066005.1; 153,059 bp; 132 genes
drSmyPerf1oatk.readsmito2023-02-1615,837FalseOP801828.1; bp; 0 genes
drSmyPerf1oatk.readspltd2023-02-16153,384110rps16TrueNC_066005.1; 153,059 bp; 132 genes
WTSI

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