Tree of Life QC

Info

NCBI taxon id: 9612
Order: Carnivora
Family: Canidae
NCBI lineage: Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Laurasiatheria;Carnivora;Caniformia;Canidae;Canis;
GoaT genome size (M): 2,748 (direct)
GoaT asm span (M): 2,342 (direct)
GoaT chr no.: 78 (direct)
GoaT ploidy: 2 (ancestor)
ToLID prefix: mCanLup

Specimens

Below is information about specimens collected for this species retrieved from the Golden Record manifest.

Loading, please wait
public_name
specimen_id
gal
sex
organism_part
biosample
biospecimen
mCanLor1SAN0001280SANGER INSTITUTEMALEMUSCLESAMEA7532750SAMEA7532739
mCanLor1SAN0001280SANGER INSTITUTEMALEMUSCLESAMEA7532749SAMEA7532739
mCanLor1SAN0001280SANGER INSTITUTEMALEMUSCLESAMEA7532748SAMEA7532739
Showing 1 to 3 of 3 rows

Spectra estimates

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope.

Loading, please wait
source
specimen
k-mer
k-cov
haploid size
repeat (%)
heterozygosity (%)
model fit (%)
model error (%)
histogram
hic-dovetailmCanLor13114.073,104,376,5680.00100.0012.250.34
illuminamCanLor131222,294,693,48611.540.4496.630.19
10xmCanLor131372,289,301,72318.100.5698.930.48
pacbiomCanLor13116.42,311,764,90411.410.3697.810.22

Sequence data

PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

Loading, please wait
pipeline
specimen
date
run id
movie
well
tag
yield
N50
sample accession
run accession
barcode
PacBio - HiFimCanLor12020-09-10TRACTION-RUN-47m64016_200910_161534A01100113,327,667,23913,728SAMEA7532748ERR6406204
PacBio - HiFimCanLor12020-09-17TRACTION-RUN-50m64089_200917_151241A01100114,121,878,41712,332SAMEA7532748ERR6406205
PacBio - HiFimCanLor12020-10-03TRACTION-RUN-54m64094_201003_145620C01100113,907,677,24413,219SAMEA7532748ERR6412029
PacBio - HiFimCanLor12020-10-04TRACTION-RUN-54m64094_201004_152428D01100114,622,934,41412,662SAMEA7532748ERR6412030
PacBio - HiFimCanLor12020-10-14TRACTION-RUN-59m64094_201014_175437A01100113,266,144,04014,461SAMEA7532748ERR6412359
PacBio - HiFimCanLor12020-10-15TRACTION-RUN-59m64094_201015_180930B01100112,112,207,22714,096SAMEA7532748ERR6412360
Showing 1 to 6 of 6 rows

Illumina run data

Illumina run stats.

Loading, please wait
pipeline
specimen
date
run id
read pairs
yield
sample accession
run accession
run status
barcode
-mCanLor1-mCanLor1_P12105_202_S88_L005802,027,450121,106,144,950SAMEA7532748ERR6511153-Canis lupus (1.00)
-mCanLor1-mCanLor1_P6307_102_S2_L002884,723,254133,593,211,354SAMEA7532748ERR6511152-Canis lupus lupus (1.00)
Chromium genomemCanLor12020-03-1733766_7#1252,698,43838,157,464,138SAMEA7532748ERR6054484qc completeCanis lupus (1.00)
Chromium genomemCanLor12020-03-1733766_7#4234,019,81435,336,991,914SAMEA7532748ERR6054487qc completeCanis lupus familiaris (1.00)
Chromium genomemCanLor12020-03-1733766_8#4234,251,76435,372,016,364SAMEA7532748ERR6054491qc completeCanis lupus familiaris (1.00)
Chromium genomemCanLor12020-03-1733766_7#2202,561,48030,586,783,480SAMEA7532748ERR6054485qc completeCanis lupus lupus (1.00)
Chromium genomemCanLor12020-03-1733766_8#2203,243,90430,689,829,504SAMEA7532748ERR6054489qc completeCanis lupus familiaris (1.00)
Chromium genomemCanLor12020-03-1733766_8#1252,234,34638,087,386,246SAMEA7532748ERR6054488qc completeCanis lupus familiaris (1.00)
Chromium genomemCanLor12020-03-1733766_8#3208,486,65831,481,485,358SAMEA7532748ERR6054490qc completeCanis lupus lupus (1.00)
Chromium genomemCanLor12020-03-1733766_7#3208,206,30031,439,151,300SAMEA7532748ERR6054486qc completeCanis lupus familiaris (1.00)
RNA-seq dUTP eukaryoticmCanLor12021-02-2436520_1#124,947,3323,742,099,800SAMEA7532748ERR6054492qc completeCanis lupus lupus (1.00)
Showing 1 to 11 of 11 rows
1025
 rows per page

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.

Loading, please wait
identity
info
0.99756[3268 seqs] NC_006583.3 Canis lupus familiaris breed boxer chromosome 1, CanFam3.1, whole genome shotgun sequence [...]
0.929212NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.905377[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.905377[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.903832NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence
0.902507[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.902507[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...]
0.900615[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.900615NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.900227[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
Showing 1 to 10 of 11 rows
1025
 rows per page

Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

Loading, please wait
specimen
contig
SSU length
attributed taxonomy by SSU
No matching records found

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.

Loading, please wait
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.

Loading, please wait
specimen
visualisation
mCanLor1

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.

    Loading, please wait
    specimen
    asm
    date
    contig N50
    contigs
    scaffold N50
    scaffolds
    length
    BUSCO
    merqury
    mCanLor1hifiasm.scaffolding.test.salsa2020-10-1735,086,44642853,617,4503282,455,261,512-
    mCanLor1hifiasm2020-10-1737,022,1375352,470,798,198C:96.1%[S:94.8%,D:1.3%],F:1.7%,M:2.2%,n:4104-
    mCanLor1hifiasm.purging2020-10-1737,022,1374122,455,253,943C:96.2%[S:94.9%,D:1.3%],F:1.7%,M:2.1%,n:4104-
    mCanLor1hifiasm.scaffolding.salsa2020-10-1735,086,44642856,745,4073192,455,266,012-
    mCanLor1hicanu2020-10-171,895,69613,8674,035,917,676C:94.5%[S:50.2%,D:44.3%],F:2.2%,M:3.3%,n:4104-
    mCanLor1hicanu.purging2020-10-175,407,8591,2972,430,593,930C:95.5%[S:94.2%,D:1.3%],F:2.2%,M:2.3%,n:4104-

    Organelles

    In-progress organelle results from MitoHiFi or Oatk.

    Loading, please wait
    specimen
    asm
    organelle
    date
    length
    genes
    frameshifts
    is circular
    reference
    No matching records found
    WTSI

    Tree of Life Species Report is developed within the Tree of Life Programme at the Wellcome Sanger Institute
    Copyright © 2020-2022 Genome Research Limited (reg no. 2742969) is a charity registered in England with number 1021457.
    Terms and conditions | Cookies policy.