Tree of Life QC: Species Report - Agriphila geniculea

NCBI taxon id:	1660579 NCBI; ENA; GoaT
Order:	Lepidoptera
Family:	Crambidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Pyraloidea;Crambidae;Crambinae;Agriphila;
GoaT genome size (M):	601 (ancestor)
GoaT asm span (M):	781 (direct)
GoaT chr no.:	34 (ancestor)
GoaT haploid no.:	17 (ancestor)
GoaT ploidy:	2 (ancestor)
ToLID prefix:	ilAgrGeni

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

tolid	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilAgrGeni1	Ox000949	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA8603615	SAMEA8603180

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
10x	ilAgrGeni1	31	29.62	859,594,105	58.99	1.83	98.31	0.49	histogram.txt
pacbio	ilAgrGeni1	31	12.93	771,188,328	52.21	1.67	97.88	0.18	histogram.txt
hic-arima2	ilAgrGeni1	31	11.51	4,601,581,547	0.00	100.00	10.98	0.19	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilAgrGeni1	2021-05-28	82781	m64222e_210528_183040	B01	1008	21,119,129,888	15,584	SAMEA8603615	ERR8978464

id	taxon	similarity	seq	country	latitude	longitude
LON6518-17	Agriphila geniculea	1	COI-5P	Norway	58.3896	8.71272
LON4062-16	Agriphila geniculea	1	COI-5P	Norway	58.0735	8.05335
CGUKB641-09	Agriphila geniculea	1	COI-5P	United Kingdom	[object Object]	[object Object]
CGUKC124-09	Agriphila geniculea	1	COI-5P	United Kingdom	51.36	-0.09
CGUKC653-09	Agriphila geniculea	1	COI-5P	United Kingdom	51.62	0.04
CGUKD1046-09	Agriphila geniculea	1	COI-5P	United Kingdom	50.396	-4.051
PYRG397-11	Lepidoptera	1	COI-5P	Germany	51.833	14.45
EUPYR077-11	Lepidoptera	1	COI-5P	Netherlands	53.45	5.61667
LEEUA280-11	Agriphila geniculea	1	COI-5P	Denmark	[object Object]	[object Object]
NLLEA1083-12	Agriphila geniculea	1	COI-5P	Netherlands	52.157	4.38

pipeline	specimen	date	run id	flowcell	type	yield	N50	sample accession	report
No matching records found

Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Chromium genome	ilAgrGeni1	2021-06-28	38911_1#33	137,718,672	20,795,519,472	SAMEA8603615	ERR8702827	qc complete	Agriphila geniculea (1.00)
Chromium genome	ilAgrGeni1	2021-06-28	38911_1#35	153,741,808	23,215,013,008	SAMEA8603615	ERR8702829	qc complete	Agriphila geniculea (1.00)
Chromium genome	ilAgrGeni1	2021-06-28	38911_1#36	121,369,808	18,326,841,008	SAMEA8603615	ERR8702830	qc complete	Agriphila geniculea (1.00)
Chromium genome	ilAgrGeni1	2021-06-28	38911_1#34	128,659,734	19,427,619,834	SAMEA8603615	ERR8702828	qc complete	Agriphila geniculea (1.00)
Hi-C - Arima v2	ilAgrGeni1	2021-06-04	38212_3#4	920,066,688	138,930,069,888	SAMEA8603615	ERR8702826	qc complete	Agriphila geniculea (1.00)

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
0.999666	[120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...]
0.988778	[5 seqs] NZ_LMOU01000001.1 Microbacterium sp. Leaf159 contig_1, whole genome shotgun sequence [...]
0.984479	[5 seqs] NZ_CM004290.1 Pantoea sp. OXWO6B1 plasmid unnamed1, whole genome shotgun sequence [...]
0.981596	[75 seqs] NZ_MJGN01000001.1 Curtobacterium sp. MCBA15_008 MCBA15_008_contig_1, whole genome shotgun sequence [...]
0.979767	NZ_CP017674.1 Microbacterium sp. BH3-3-3, complete genome
0.959641	[16 seqs] NZ_MPLD01000001.1 Pseudomonas koreensis strain CI12 Contig_01, whole genome shotgun sequence [...]
0.929624	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.910001	[608 seqs] NZ_MAYS01000001.1 Candidatus Erwinia dacicola strain IL contig_1, whole genome shotgun sequence [...]
0.903242	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.901381	[6 seqs] NZ_LMRB01000001.1 Microbacterium sp. Leaf436 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
ilAgrGeni1	atg000706l	1867	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;
ilAgrGeni1	ptg000176l	1520	ENA: Bacteria;Actinobacteria;Micrococcales;Microbacteriaceae;Microbacterium; SILVA: Bacteria;Actinobacteriota;Actinobacteria;Micrococcales;Microbacteriaceae;Microbacterium;
ilAgrGeni1	ptg000236l	1537	ENA: Bacteria;Proteobacteria;Gammaproteobacteria; SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Pantoea;
ilAgrGeni1	ptg000261l	1519	ENA: Bacteria;Actinobacteria;Micrococcales;Microbacteriaceae;Microbacterium; SILVA: Bacteria;Actinobacteriota;Actinobacteria;Micrococcales;Microbacteriaceae;Microbacterium;
ilAgrGeni1	ptg000480l	1525	ENA: Bacteria;Actinobacteria;Micrococcales;Microbacteriaceae;Curtobacterium; SILVA: Bacteria;Actinobacteriota;Actinobacteria;Micrococcales;Microbacteriaceae;Curtobacterium;
ilAgrGeni1	ptg000482l	1813	ENA: Eukaryota;Metazoa;Ecdysozoa;Nematoda;Enoplea;Dorylaimia;Mermithida;Mermithoidea;Mermithidae;unclassified Mermithidae; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Nematozoa;Nematoda;Enoplea;Dorylaimia;Mermithida;
ilAgrGeni1	ptg000504l	1882	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;
ilAgrGeni1	ptg000533l	1873	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;
ilAgrGeni1	ptg000562c	1887	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;
ilAgrGeni1	ptg000585l	1904	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;

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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
specimen	family	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
ilAgrGeni1

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

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
ilAgrGeni1	hicanu.purging	2021-08-21	1,776,407	1,181			851,426,439	C:98.8%[S:94.7%,D:4.1%],F:0.4%,M:0.8%,n:1367	Q40.9-C95.0(10X)
ilAgrGeni1	hicanu	2021-08-21	1,247,175	3,866			1,571,553,388	C:98.9%[S:50.3%,D:48.6%],F:0.4%,M:0.7%,n:1367	Q40.8-C95.2(10X)
ilAgrGeni1	hifiasm.purging	2021-08-21	7,678,319	385			808,636,641	C:98.3%[S:97.1%,D:1.2%],F:0.5%,M:1.2%,n:1367	Q40.8-C94.9(10X)
ilAgrGeni1	hifiasm.scaff.salsa	2021-08-21	6,993,363	403	24,502,928	282	808,686,931		-
ilAgrGeni1	hifiasm.scaff.yahs	2021-08-21	6,996,000	402	26,137,137	250	808,656,831		-
ilAgrGeni1	hifiasm	2021-08-21	7,274,048	719			857,115,834	C:98.5%[S:95.2%,D:3.3%],F:0.5%,M:1.0%,n:1367	Q39.9-C95.0(10X)

Agriphila geniculea

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

Assemblies

Organelles

Agriphila geniculea

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification