Tree of Life QC

Info

NCBI taxon id: 988081  NCBI; ENA; GoaT
Order: Lepidoptera
Family: Noctuidae
NCBI lineage: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Noctuoidea;Noctuidae;Xyleninae;Brachylomia;
GoaT genome size (M): 655 (ancestor)
GoaT asm span (M): 782 (direct)
GoaT chr no.: 31 (ancestor)
GoaT haploid no.: 30 (ancestor)
GoaT ploidy: 2 (ancestor)
ToLID prefix: ilBraVimi

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
ilBraVimi1Ox000522UNIVERSITY OF OXFORDNOT_COLLECTEDTHORAXSAMEA7701377SAMEA7701291
ilBraVimi1Ox000522UNIVERSITY OF OXFORDNOT_COLLECTEDHEADSAMEA7701377SAMEA7701291
ilBraVimi1Ox000522UNIVERSITY OF OXFORDNOT_COLLECTEDABDOMENSAMEA7701378SAMEA7701291
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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
10xilBraVimi13138.81849,061,90943.641.2198.200.41
histogram.txt
pacbioilBraVimi13123.75734,710,16835.881.2898.220.15
histogram.txt
hic-arima2ilBraVimi13121.111,698,698,2930.00100.0013.690.13
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 - HiFiilBraVimi12021-05-1482321m64094e_210514_221021B01100214,303,748,75213,833SAMEA7701378ERR9127942
PacBio - HiFi (ULI)ilBraVimi12022-02-13TRACTION-RUN-71m64229e_220213_031624C01-22,365,681,7367,884SAMEA7701378ERR9468771
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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 genomeilBraVimi12021-06-1638403_2#10179,783,64827,147,330,848SAMEA7701378ERR9123825qc completeBrachylomia viminalis (1.00)
Chromium genomeilBraVimi12021-06-1638403_2#12167,260,44825,256,327,648SAMEA7701378ERR9123827qc completeBrachylomia viminalis (1.00)
Chromium genomeilBraVimi12021-06-1638403_2#11155,030,48423,409,603,084SAMEA7701378ERR9123826qc completeBrachylomia viminalis (1.00)
Chromium genomeilBraVimi12021-06-1638403_2#9181,956,97427,475,503,074SAMEA7701378ERR9123824qc completeBrachylomia viminalis (1.00)
Hi-C - Arima v2ilBraVimi12021-05-1637941_1#8612,239,53092,448,169,030SAMEA7701377ERR9123823qc completeBrachylomia viminalis (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
0.962383[50 seqs] NZ_MIKA01000001.1 Enterococcus plantarum strain LMG 26214, whole genome shotgun sequence [...]
0.924425[2 seqs] NC_009832.1 Serratia proteamaculans 568, complete genome [...]
0.91934NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.917245NZ_CP011254.1 Serratia fonticola strain DSM 4576, complete genome
0.912446[2 seqs] NZ_KB661119.1 Serratia sp. S4 SerS4DRAFT_SSJ.1, whole genome shotgun sequence [...]
0.910625[64 seqs] NZ_JRFX01000001.1 Lactococcus lactis strain Bpl1 NODE_47, whole genome shotgun sequence [...]
0.906067[32 seqs] NZ_KN050720.1 Rahnella sp. WP5 EX31DRAFT_scaffold00001.1, whole genome shotgun sequence [...]
0.905028[608 seqs] NZ_MAYS01000001.1 Candidatus Erwinia dacicola strain IL contig_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
ilBraVimi1atg000154l881
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilBraVimi1atg000463l889
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilBraVimi1ptg000046l1898
  • ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;
  • SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilBraVimi1ptg000156l1538
  • ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Yersiniaceae;
  • SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Yersiniaceae;
ilBraVimi1ptg000176l1484
  • ENA: Bacteria;Proteobacteria;Alphaproteobacteria;Rhodospirillales;Acetobacteraceae;environmental samples;
  • SILVA: Bacteria;Proteobacteria;Alphaproteobacteria;Acetobacterales;Acetobacteraceae;Commensalibacter;
ilBraVimi1ptg000188l2198
  • ENA: Eukaryota;Euglenozoa;Kinetoplastida;Trypanosomatidae;Leishmaniinae;
  • SILVA: Eukaryota;Discoba;Discicristata;Euglenozoa;Kinetoplastea;Metakinetoplastina;Trypanosomatida;
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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
ilBraVimi1Acetobacteraceae9620.02C:84.4%[S:29.5%,D:54.9%],F:3.4%,M:12.2%,n:617C:5.5%[S:5.5%,D:0.0%],F:0.0%,M:94.5%,n:61760.11Mb77C:45.7%[S:45.2%,D:0.5%],F:4.2%,M:50.1%,n:617481.33Mb440
ilBraVimi1Trypanosomatidae6,5500C:75.4%[S:46.2%,D:29.2%],F:12.3%,M:12.3%,n:130C:0.0%[S:0.0%,D:0.0%],F:0.0%,M:100.0%,n:13010.01Mb82C:1.5%[S:1.5%,D:0.0%],F:1.5%,M:97.0%,n:13060.12Mb41
ilBraVimi1Yersiniaceae5,2770.12C:99.5%[S:2.5%,D:97.0%],F:0.5%,M:0.0%,n:440C:11.4%[S:10.7%,D:0.7%],F:1.8%,M:86.8%,n:440480.89Mb740C:79.3%[S:45.9%,D:33.4%],F:4.8%,M:15.9%,n:4402276.35Mb2,313
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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
ilBraVimi1

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

  • ilBraVimi1.hifiasm.20220815

Assemblies

In-progress assembly QC.

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specimen
asm
date
contig N50
contigs
scaffold N50
scaffolds
length
BUSCO
merqury
ilBraVimi1hifiasm.polishing_2022-02-1919,879,860156784,545,475C:99.1%[S:98.2%,D:0.9%],F:0.4%,M:0.5%,n:1367Q51.1-C97.0(10X); Q57.6-C99.0(HiFi)
ilBraVimi1hifiasm.purging2022-02-1919,879,997156784,549,111C:99.1%[S:98.2%,D:0.9%],F:0.4%,M:0.5%,n:1367Q50.1-C97.0(10X); Q64.7-C99.0(HiFi)
ilBraVimi1hifiasm.scaff.salsa2022-02-1919,879,99716125,552,651143784,558,111-
ilBraVimi1hifiasm.scaff.yahs2022-02-1919,879,99716726,537,898128784,556,911-
ilBraVimi1hifiasm2022-02-1919,879,997246796,626,991C:99.0%[S:97.5%,D:1.5%],F:0.4%,M:0.6%,n:1367Q49.9-C97.1(10X); Q64.3-C99.1(HiFi)
ilBraVimi1hifiasm.scaffolding.salsa2022-02-1919,879,86016125,552,511143784,554,475C:99.0%[S:98.3%,D:0.7%],F:0.4%,M:0.6%,n:1367Q51.1-C97.0(10X); Q57.6-C99.0(HiFi)
ilBraVimi1hifiasm.scaffolding.yahs2022-02-1919,879,86016626,537,765127784,553,275C:99.1%[S:98.4%,D:0.7%],F:0.4%,M:0.5%,n:1367Q51.1-C97.0(10X); Q57.6-C99.0(HiFi)
ilBraVimi1hicanu2022-02-191,815,7213,1161,562,521,308C:99.2%[S:5.9%,D:93.3%],F:0.4%,M:0.4%,n:1367Q47.0-C97.1(10X); Q71.0-C99.1(HiFi)
ilBraVimi1hicanu.purging2022-02-192,432,579715798,384,924C:99.0%[S:96.9%,D:2.1%],F:0.5%,M:0.5%,n:1367Q51.3-C97.0(10X); Q72.6-C99.0(HiFi)
ilBraVimi1hifiasm-hic2022-08-1520,894,109372805,231,887C:99.1%[S:97.1%,D:2.0%],F:0.4%,M:0.5%,n:1367Q46.6-C97.1(10X); Q64.8-C99.1(HiFi)
ilBraVimi1hifiasm.purging2022-08-1520,894,109261789,376,047C:99.1%[S:98.2%,D:0.9%],F:0.4%,M:0.5%,n:1367Q46.7-C97.0(10X); Q65.2-C99.0(HiFi)
ilBraVimi1hifiasm2022-08-1520,894,109371805,226,659C:99.1%[S:97.1%,D:2.0%],F:0.4%,M:0.5%,n:1367Q46.6-C97.1(10X); Q64.8-C99.1(HiFi)
ilBraVimi1hifiasm.scaffolding.salsa2022-08-1518,908,82327626,043,442255789,386,547C:99.1%[S:98.2%,D:0.9%],F:0.4%,M:0.5%,n:1367Q46.7-C97.0(10X); Q65.2-C99.0(HiFi)
ilBraVimi1hifiasm.scaffolding.yahs2022-08-1520,659,21126627,028,656229789,383,447C:99.0%[S:98.2%,D:0.8%],F:0.4%,M:0.6%,n:1367Q46.7-C97.0(10X); Q65.2-C99.0(HiFi)
ilBraVimi1hicanu2022-08-152,279,8623,5661,577,153,816C:99.2%[S:5.9%,D:93.3%],F:0.4%,M:0.4%,n:1367Q45.0-C99.8(10X); Q72.3-C100.0(HiFi)
ilBraVimi1hicanu.purging2022-08-153,317,846742798,986,246C:99.1%[S:97.1%,D:2.0%],F:0.4%,M:0.5%,n:1367Q46.0-C97.1(10X); Q73.5-C99.1(HiFi)

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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specimen
asm
organelle
date
length
genes
frameshifts
is circular
reference
ilBraVimi1mitohifi.hifiasmmito2022-02-1929,94956NoneMW697903.1; 15,347 bp; 37 genes
ilBraVimi1mitohifi.hicanumito2022-02-1932,56058NoneMW697903.1; 15,347 bp; 37 genes
ilBraVimi1mitohifi.readsmito2022-02-1916,44737ND2MW697903.1; 15,347 bp; 37 genes
ilBraVimi1mitohifi.hifiasm-hicmito2022-08-1516,41037NoneTrueOM140690.1; 15,441 bp; 37 genes
ilBraVimi1mitohifi.hifiasmmito2022-08-1516,41037NoneTrueOM140690.1; 15,441 bp; 37 genes
ilBraVimi1mitohifi.hicanumito2022-08-1516,15637ND2TrueOM140690.1; 15,441 bp; 37 genes
ilBraVimi1mitohifi.readsmito2022-08-1516,15037NoneTrueOM140690.1; 15,441 bp; 37 genes
WTSI

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