Tree of Life QC: Species Report

NCBI taxon id:	2803876 NCBI; ENA; GoaT
Order:	Opiliones
Family:	Phalangiidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;Palpatores;Phalangioidea;Phalangiidae;Odiellus;
GoaT genome size (M):	1,100 (ancestor)
GoaT asm span (M):	443 (direct)
GoaT chr no.:	32 (ancestor)
GoaT haploid no.:	8 (ancestor)
GoaT ploidy:	6 (ancestor)
ToLID prefix:	qqOdiSpin

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
qqOdiSpin1	NHMUK014447001	NATURAL HISTORY MUSEUM	NOT_COLLECTED	LEG	SAMEA9066101	SAMEA9066027
qqOdiSpin1	NHMUK014447001	NATURAL HISTORY MUSEUM	NOT_COLLECTED	ABDOMEN	SAMEA9066100	SAMEA9066027
qqOdiSpin1	NHMUK014447001	NATURAL HISTORY MUSEUM	NOT_COLLECTED	CEPHALOTHORAX	SAMEA9066099	SAMEA9066027
qqOdiSpin2	NHMUK014447000	NATURAL HISTORY MUSEUM	NOT_COLLECTED	ABDOMEN	SAMEA9066098	SAMEA9066026
qqOdiSpin2	NHMUK014447000	NATURAL HISTORY MUSEUM	NOT_COLLECTED	CEPHALOTHORAX	SAMEA9066097	SAMEA9066026

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
hic-arima2	qqOdiSpin2	31	51.27	1,066,995,835	0.00	100.00	2.35	0.15	histogram.txt
pacbio	qqOdiSpin1	31	26.86	469,181,192	47.48	0.27	97.06	0.12	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	qqOdiSpin1	2021-07-12	84271	m64174e_210712_144141	D01	1001	2,230,184,535	11,928	SAMEA9066099	ERR10809389
PacBio - HiFi	qqOdiSpin1	2022-12-13	TRACTION-RUN-375	m64016e_221213_110948	F01	1022	23,956,738,671	13,197	SAMEA9066100	ERR10809388

id	taxon	similarity	seq	country	latitude	longitude
SMNSA179-16	Odiellus spinosus	1	COI-5P	Germany	52.19	12.38
SMNSA168-16	Odiellus spinosus	0.9969	COI-5P	Germany	52.33	11.6
SMNSA197-16	Odiellus spinosus	0.9969	COI-5P	Germany	52.1	12.7
SMNSA217-16	Odiellus spinosus	0.9969	COI-5P	Germany	52.24	12.62
GBMYR614-15	Opiliones	0.9969	COI-5P	Germany	50.931	11.6
SMNSA196-16	Odiellus spinosus	0.9954	COI-5P	Germany	52.1	12.7
SMNSA024-16	Paroligolophus agrestis	0.8968	COI-5P	Germany	52.33	11.6
GBBSP833-15	Paroligolophus agrestis	0.894	COI-5P	Germany	53.79	10.7
GBBSP1793-15	Paroligolophus agrestis	0.894	COI-5P	Germany	53.71	8.8
GBBSP1794-15	Paroligolophus agrestis	0.894	COI-5P	Germany	53.71	8.8

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
Hi-C - Arima v2	qqOdiSpin2	2023-01-19	46585_3#4	948,407,996	143,209,607,396	SAMEA9066097	ERR10802466	qc complete
RNA PolyA	qqOdiSpin3	2023-02-10	46644_1#28	61,597,416	9,301,209,816	SAMEA9066096	ERR10890709	qc complete	Odiellus spinosus (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
0.922314	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete 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
qqOdiSpin1	atg001490l	1458	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;Palpatores;Phalangioidea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;
qqOdiSpin1	atg001739l	1813	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;Palpatores; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;
qqOdiSpin1	ptg000048l	1311	ENA: Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;Palpatores;Phalangioidea; SILVA: Eukaryota;Amorphea;Obazoa;Opisthokonta;Holozoa;Choanozoa;Metazoa;Animalia;BCP clade;Bilateria;Protostomia;Ecdysozoa;Arthropoda;Chelicerata;Arachnida;Opiliones;

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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
qqOdiSpin1

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

qqOdiSpin1.hifiasm.20221215

BTK datasets:

qqOdiSpin1.20230120.fa.ascc qqOdiSpin1-MT.fa.ascc qqOdiSpin1.20230120.haplotigs.fa.ascc

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
qqOdiSpin1	hicanu.purging	2022-12-15	2,944,281	1,076			479,082,324	C:96.9%[S:96.5%,D:0.4%],F:2.1%,M:1.0%,n:1013	Q66.1-C98.7(HiFi)
qqOdiSpin1	hicanu	2022-12-15	685,748	9,276			1,023,813,316	C:97.1%[S:33.0%,D:64.1%],F:2.0%,M:0.9%,n:1013	Q66.1-C100.0(HiFi)
qqOdiSpin1	hifiasm.purging	2022-12-15	3,993,738	422			445,112,795	C:97.0%[S:96.6%,D:0.4%],F:2.0%,M:1.0%,n:1013	Q60.6-C98.4(HiFi)
qqOdiSpin1	hifiasm	2022-12-15	3,377,377	641			569,150,931	C:97.0%[S:96.4%,D:0.6%],F:2.0%,M:1.0%,n:1013	Q61.0-C98.9(HiFi)
qqOdiSpin1	hifiasm.scaffolding.salsa	2022-12-15	3,578,868	472	6,732,986	364	445,166,795	C:97.0%[S:96.6%,D:0.4%],F:2.0%,M:1.0%,n:1013	Q60.6-C98.4(HiFi)
qqOdiSpin1	hifiasm.scaffolding.yahs	2022-12-15	3,575,313	541	21,628,951	327	445,155,595	C:97.0%[S:96.6%,D:0.4%],F:2.0%,M:1.0%,n:1013	Q60.6-C98.4(HiFi)

specimen	asm	organelle	date	length	genes	frameshifts	is circular	reference
qqOdiSpin1	mitohifi.hicanu	mito	2022-12-15	16,081	36	None	True	NC_029887.1; 16,798 bp; 37 genes
qqOdiSpin1	mitohifi.reads	mito	2022-12-15	16,074	36	None	True	NC_029887.1; 16,798 bp; 37 genes
qqOdiSpin1	mitohifi.hifiasm	mito	2022-12-15	16,074	36	None	True	NC_029887.1; 16,798 bp; 37 genes

Odiellus spinosus

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

qqOdiSpin1.hifiasm.20221215

Assemblies

Organelles

Odiellus spinosus

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

qqOdiSpin1.hifiasm.20221215

BlobToolKit