Tree of Life QC: Species Report - Archips xylosteana

Info

NCBI taxon id:	1100919 NCBI; ENA; GoaT
Order:	Lepidoptera
Family:	Tortricidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Tortricoidea;Tortricidae;Tortricinae;Archips;
GoaT genome size (M):	600 (ancestor)
GoaT asm span (M):	650 (direct)
GoaT chr no.:	30 (ancestor)
GoaT haploid no.:	30 (ancestor)
GoaT ploidy:	2 (ancestor)
ToLID prefix:	ilArcXylo

tolid	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilArcXylo1	Ox000680	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7701730	SAMEA7701541
ilArcXylo2	Ox001601	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA10978866	SAMEA10978768
ilArcXylo3	NHMUK013698377	NATURAL HISTORY MUSEUM	MALE	WHOLE_ORGANISM	SAMEA114805807	SAMEA114805688

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
hic-arima2	ilArcXylo2	31	75.69	508,002,060	200.91	62.39	98.38	0.39	histogram.txt
pacbio	ilArcXylo1	31	20.44	611,917,029	40.29	1.14	98.49	0.19	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilArcXylo1	2021-02-28	80157	m64178e_210228_143923	C01	1018	26,554,861,463	15,486	SAMEA7701730	ERR10287579

id	taxon	similarity	seq	country	latitude	longitude
CGUKC1024-09	Archips xylosteana	0.9969	COI-5P	United Kingdom	51.62	0.04
GBLAA1571-15	Lepidoptera	0.9985	COI-5P	Germany	52.981	13.824
FGMLD392-13	Lepidoptera	0.9969	COI-5P	Germany	52.174	13.5626
TONA436-08	Archips xylosteana	0.9954	COI-5P	Canada	[object Object]	[object Object]
LON3058-16	Archips xylosteana	0.9939	COI-5P	Norway	59.073	10.061
FBLMU056-09	Archips xylosteana	0.9939	COI-5P	Germany	49.0314	12.1561
NLLEA654-12	Archips xylosteana	0.9939	COI-5P	Netherlands	52.157	4.38
NLLEA643-12	Archips xylosteana	0.9924	COI-5P	Netherlands	52.157	4.38
NLLEA658-12	Archips xylosteana	0.9924	COI-5P	Netherlands	52.157	4.38
NLLEA680-12	Archips xylosteana	0.9924	COI-5P	Netherlands	52.157	4.38

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

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Hi-C - Arima v2	ilArcXylo2	2022-09-16	45817_1#3	718,571,412	108,504,283,212	SAMEA10978866	ERR10297859	qc complete	Archips xylosteana (1.00)
RNA PolyA	ilArcXylo3	2024-08-07	49280_1#36	94,657,966	14,293,352,866	SAMEA114805807		archival in progress	Archips xylosteana (1.00)

identity	info
0.957191	[42 seqs] NZ_MIKC01000001.1 Enterococcus ureilyticus strain LMG 26676, whole genome shotgun sequence [...]
0.935399	[19 seqs] NZ_MIJZ01000001.1 Enterococcus ureasiticus strain DSM 23328, whole genome shotgun sequence [...]
0.922314	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.910001	[32 seqs] NZ_KN050720.1 Rahnella sp. WP5 EX31DRAFT_scaffold00001.1, whole genome shotgun sequence [...]

specimen	contig	SSU length	attributed taxonomy by SSU
ilArcXylo1	ptg000034l	1904	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Holometabola;Lepidoptera;Glossata;Ditrysia; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Amphiesmenoptera;Lepidoptera;
ilArcXylo1	ptg000069l	1538	ENA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Yersiniaceae; SILVA: Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Yersiniaceae;

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
ilArcXylo1	Yersiniaceae	1,679	0.09	C:86.4%[S:25.5%,D:60.9%],F:8.2%,M:5.4%,n:440	C:56.6%[S:56.4%,D:0.2%],F:4.8%,M:38.6%,n:440	65	2.67Mb	1,108	C:67.7%[S:67.5%,D:0.2%],F:5.5%,M:26.8%,n:440	65	4.24Mb	342

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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
ilArcXylo1

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

ilArcXylo1.hifiasm.20220916

BTK datasets:

ilArcXylo1Pri ilArcXylo1Hap

Assemblies

In-progress assembly QC.

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specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
ilArcXylo1	hicanu.purging	2021-03-04	9,260,553	269			662,489,573	C:98.8%[S:98.2%,D:0.6%],F:0.5%,M:0.7%,n:1367	Q72.9-C98.9(HiFi)
ilArcXylo1	hicanu	2021-03-04	4,189,850	2,486			1,297,083,666	C:98.9%[S:63.2%,D:35.7%],F:0.5%,M:0.6%,n:1367	Q70.5-C98.9(HiFi)
ilArcXylo1	hifiasm.purging	2021-03-04	23,784,757	115			677,323,485	C:98.7%[S:97.1%,D:1.6%],F:0.7%,M:0.6%,n:1367	Q66.4-C98.8(HiFi)
ilArcXylo1	hifiasm	2021-03-04	22,564,248	198			734,596,355	C:98.7%[S:94.4%,D:4.3%],F:0.7%,M:0.6%,n:1367	Q65.7-C98.9(HiFi)
ilArcXylo1	hicanu.purging	2022-09-16	7,499,703	300			661,109,178	C:98.7%[S:98.2%,D:0.5%],F:0.5%,M:0.8%,n:1367	Q69.3-C98.5(HiFi)
ilArcXylo1	hicanu	2022-09-16	3,638,009	2,310			1,289,027,948	C:98.8%[S:10.4%,D:88.4%],F:0.5%,M:0.7%,n:1367	Q67.7-C100.0(HiFi)
ilArcXylo1	hifiasm.purging_e	2022-09-16	20,380,096	170			653,012,166	C:98.8%[S:98.2%,D:0.6%],F:0.4%,M:0.8%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm.purging	2022-09-16	21,457,628	122			661,312,323	C:98.8%[S:97.6%,D:1.2%],F:0.4%,M:0.8%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm.scaffolding.yahs	2022-09-16	21,457,628	146	22,554,109	138	661,313,923	C:98.9%[S:97.7%,D:1.2%],F:0.5%,M:0.6%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm.scaffolding.salsa	2022-09-16	21,457,628	123	22,554,109	120	661,313,823	C:98.9%[S:97.7%,D:1.2%],F:0.4%,M:0.7%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm.scaffolding_e.yahs	2022-09-16	20,368,662	192	21,687,607	172	653,016,166	C:98.9%[S:98.3%,D:0.6%],F:0.5%,M:0.6%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm.scaffolding_e.salsa	2022-09-16	20,380,096	173	21,756,703	156	653,020,666	C:98.8%[S:98.2%,D:0.6%],F:0.4%,M:0.8%,n:1367	Q64.9-C98.5(HiFi)
ilArcXylo1	hifiasm	2022-09-16	21,457,628	226			677,753,727	C:98.9%[S:95.8%,D:3.1%],F:0.4%,M:0.7%,n:1367	Q64.8-C98.6(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
ilArcXylo1	mitohifi.reads	mito	2022-09-16	16,386	37	None	True	1	MW936632.1; 15,389 bp; 37 genes
ilArcXylo1	mitohifi.hicanu	mito	2022-09-16	16,390	36	ND5	True	1	MW936632.1; 15,389 bp; 37 genes
ilArcXylo1	mitohifi.hifiasm	mito	2022-09-16	16,386	37	None	True	1	MW936632.1; 15,389 bp; 37 genes

Archips xylosteana

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

ilArcXylo1.hifiasm.20220916

Assemblies

Organelles

Archips xylosteana

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

ilArcXylo1.hifiasm.20220916

BlobToolKit