Tree of Life QC

Info

NCBI taxon id: 3486  NCBI; ENA; GoaT
Order: Rosales
Family: Cannabaceae
NCBI lineage: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;Humulus;
GoaT genome size (M): 2,865 (direct)
GoaT asm span (M): 2,488 (direct)
GoaT chr no.: 20 (direct)
GoaT haploid no.: 15 (direct)
GoaT ploidy: 3 (direct)
ToLID prefix: drHumLupu

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
drHumLupu1KDTOL10038ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522103SAMEA7522047
drHumLupu1KDTOL10038ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522105SAMEA7522047
drHumLupu1KDTOL10038ROYAL BOTANIC GARDENS KEWFEMALEFLOWERSAMEA7522101SAMEA7522047
drHumLupu1KDTOL10038ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522104SAMEA7522047
drHumLupu1KDTOL10038ROYAL BOTANIC GARDENS KEWFEMALELEAFSAMEA7522102SAMEA7522047
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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
10xdrHumLupu13120.012,597,920,12358.330.6598.100.39
histogram.txt
pacbiodrHumLupu13115.912,520,749,13954.950.4398.140.11
histogram.txt
hic-arima2drHumLupu13196.232,133,119,95853.821.0294.970.33
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 - HiFidrHumLupu12021-04-1881432m64097e_210418_023741C0110036,734,227,56517,287SAMEA7522102ERR11673235
PacBio - HiFidrHumLupu12023-06-14TRACTION-RUN-629m84047_230614_152050_s2B01203276,494,738,09912,381SAMEA7522103ERR11809134
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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 genomedrHumLupu12021-06-0137642_1#22220,724,43433,329,389,534SAMEA7522102ERR11679389qc completeHumulus lupulus (1.00)
Chromium genomedrHumLupu12021-06-0137642_1#23280,951,63642,423,697,036SAMEA7522102ERR11679390qc completeHumulus lupulus (1.00)
Chromium genomedrHumLupu12021-06-0137642_1#24238,341,52235,989,569,822SAMEA7522102ERR11679391qc completeHumulus lupulus (1.00)
Chromium genomedrHumLupu12021-06-0137642_1#21332,762,28450,247,104,884SAMEA7522102ERR11679388qc completeHumulus lupulus (1.00)
Hi-C - Arima v2drHumLupu12021-07-2839557_2#13,747,956,088565,941,369,288SAMEA7522102ERR11679392qc completeHumulus lupulus (1.00)
RNA PolyAdrHumLupu12024-04-0448729_1#3065,018,5049,817,794,104SAMEA7522103qc completeHumulus lupulus (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
0.933364[151 seqs] NZ_JICM01000001.1 Acinetobacter sp. ETR1 contig_1, whole genome shotgun sequence [...]
0.932021NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.917245[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.913621NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.912743[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.912446NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.910625[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.909049[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.909049[641 seqs] NW_015449489.1 Tetranychus urticae unplaced genomic scaffold, ASM23943v1 scaffold_222, whole genome shotgun sequence [...]
0.906067NC_033778.1 Leptopilina boulardi filamentous virus isolate Valence Gotheron, partial genome
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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
drHumLupu1atg000109l1486
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1atg002077l1487
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1atg005496l689
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Rosales;Cannabis;
drHumLupu1atg017133l1191
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1atg017468l1791
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;
  • SILVA: Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;Rosales;Cannabis;
drHumLupu1ptg000009l1271
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1ptg000027l1179
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1ptg000028l1487
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1ptg000031l1158
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
drHumLupu1ptg000044l1445
  • ENA: Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliophyta;eudicotyledons;Gunneridae;Pentapetalae;rosids;fabids;Rosales;Cannabaceae;Humulus;
  • SILVA: Bacteria;Cyanobacteria;Cyanobacteriia;Chloroplast;
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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
drHumLupu1

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

  • drHumLupu1.hifiasm.20230627

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
drHumLupu1hifiasm-hic.purging2023-06-2716,473,2355082,356,788,332C:94.9%[S:92.0%,D:2.9%],F:0.4%,M:4.7%,n:2326Q51.7-C92.5(10X); Q64.9-C94.2(HiFi)
drHumLupu1hifiasm-hic.hap22023-06-2716,561,3466172,468,171,206C:97.4%[S:94.2%,D:3.2%],F:0.4%,M:2.2%,n:2326-
drHumLupu1hifiasm-hic.hap12023-06-2715,570,5671,2842,514,599,990C:97.8%[S:94.4%,D:3.4%],F:0.4%,M:1.8%,n:2326Q50.9-C96.7(10X); Q62.6-C98.7(HiFi)
drHumLupu1hifiasm-hic.scaffolding.yahs2023-06-2715,570,567525230,960,8812622,356,840,932C:95.0%[S:92.1%,D:2.9%],F:0.5%,M:4.5%,n:2326Q51.7-C92.5(10X); Q64.9-C94.2(HiFi)
drHumLupu1hicanu.purging2023-06-274,800,8223,812698,460,832C:60.5%[S:57.7%,D:2.8%],F:1.2%,M:38.3%,n:2326Q43.7-C37.9(10X); Q67.5-C39.1(HiFi)
drHumLupu1hicanu2023-06-274,272,55023,2264,747,715,672C:98.1%[S:16.5%,D:81.6%],F:0.4%,M:1.5%,n:2326Q43.6-C99.6(10X); Q68.2-C100.0(HiFi)
drHumLupu1hifiasm2023-06-2731,468,1181,1672,543,362,921C:97.9%[S:94.4%,D:3.5%],F:0.4%,M:1.7%,n:2326Q50.8-C96.7(10X); Q62.3-C98.7(HiFi)
drHumLupu1hifiasm.scaffolding_nopurge.yahs2023-06-2730,558,3471,182263,885,2711,0672,543,385,921C:98.0%[S:94.6%,D:3.4%],F:0.4%,M:1.6%,n:2326Q50.8-C96.7(10X); Q62.3-C98.7(HiFi)
drHumLupu1hifiasm.purging2023-06-2732,979,6823222,293,867,602C:92.7%[S:90.1%,D:2.6%],F:0.5%,M:6.8%,n:2326Q51.7-C91.4(10X); Q64.6-C93.1(HiFi)
drHumLupu1hifiasm.scaffolding.yahs2023-06-2732,979,682325224,525,5452292,293,886,802C:92.7%[S:90.0%,D:2.7%],F:0.5%,M:6.8%,n:2326Q51.7-C91.4(10X); Q64.6-C93.1(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
seqs
reference
drHumLupu1oatk.readsmito2023-06-27400,02360rpl2True1MW413894.1; 390,962 bp; 62 genes
drHumLupu1oatk.readspltd2023-06-27153,769106atpF;rps16True1NC_028032.1; 153,751 bp; 127 genes
WTSI

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