Tree of Life QC: Species Report - Psoricoptera gibbosella

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

NCBI taxon id:	1101149
Order:	Lepidoptera
Family:	Gelechiidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Gelechioidea;Gelechiidae;Gelechiinae;Psoricoptera;
GoaT genome size (M):	600 (ancestor)
GoaT asm span (M):	906 (ancestor)
GoaT chr no.:	58 (ancestor)
ToLID prefix:	ilPsoGibb

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilPsoGibb1	Ox000805	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7746699	SAMEA7746612

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

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
10x	ilPsoGibb1	31	43.07	569,414,636	42.95	1.08	96.86	0.48
pacbio	ilPsoGibb1	31	16.4	509,767,128	35.90	0.96	98.38	0.24

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilPsoGibb1	2021-04-11	81229	m64230e_210411_134214	C01	1019	18,025,608,378	15,575	SAMEA7746699

id	taxon	similarity	seq	country	latitude	longitude
LON1986-15	Psoricoptera gibbosella	1	COI-5P	Norway	58.138	8.174
FBLMT443-09	Psoricoptera gibbosella	1	COI-5P	Germany	48.5552	12.0793
FBLMV681-09	Psoricoptera gibbosella	1	COI-5P	Germany	48.9258	11.8653
PHLAC249-10	Psoricoptera gibbosella	1	COI-5P	Italy	46.428	11.3
LEFIJ1133-11	Psoricoptera gibbosella	1	COI-5P	Denmark	[object Object]	[object Object]
LEFIJ1132-11	Psoricoptera gibbosella	1	COI-5P	Denmark	[object Object]	[object Object]
LEFIJ1131-11	Psoricoptera gibbosella	1	COI-5P	Denmark	[object Object]	[object Object]
LEFIJ1130-11	Psoricoptera gibbosella	1	COI-5P	Denmark	[object Object]	[object Object]
PHLAH268-12	Psoricoptera gibbosella	1	COI-5P	Austria	47.317	9.617
LEATE562-13	Psoricoptera gibbosella	1	COI-5P	Italy	46.288	11.201

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Chromium genome	ilPsoGibb1	2021-06-01	37642_4#28	147,264,786	22,236,982,686	SAMEA7746699	qc complete	Psoricoptera gibbosella (1.00)
Chromium genome	ilPsoGibb1	2021-06-01	37642_4#25	116,344,034	17,567,949,134	SAMEA7746699	qc complete	Psoricoptera gibbosella (1.00)
Chromium genome	ilPsoGibb1	2021-06-01	37642_4#27	159,447,014	24,076,499,114	SAMEA7746699	qc complete	Psoricoptera gibbosella (1.00)
Chromium genome	ilPsoGibb1	2021-06-01	37642_4#26	97,414,276	14,709,555,676	SAMEA7746699	qc complete	Psoricoptera gibbosella (1.00)

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.

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specimen	contig	SSU length	attributed taxonomy by SSU
No matching records found

Re-assembly of reads classified under each identified SSU Marker family.

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specimen	family	classified reads			original assembly				re-assembly
specimen	family	count	(%)	BUSCO	BUSCO	contigs	contig length	reads	BUSCO	contigs	contig length	additional reads	circos
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
ilPsoGibb1

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	length	BUSCO	merqury
ilPsoGibb1	hifiasm.purging	2021-04-14	17,745,709	51	525,204,639	C:98.9%[S:98.5%,D:0.4%],F:0.3%,M:0.8%,n:1367	-
ilPsoGibb1	hifiasm	2021-04-14	17,745,709	115	559,241,177	C:99.0%[S:96.7%,D:2.3%],F:0.3%,M:0.7%,n:1367	-
ilPsoGibb1	hicanu.purging	2021-04-14	5,765,699	197	525,860,815	C:99.0%[S:98.1%,D:0.9%],F:0.4%,M:0.6%,n:1367	-
ilPsoGibb1	hicanu	2021-04-14	3,051,672	1,387	1,066,065,117	C:99.4%[S:60.6%,D:38.8%],F:0.3%,M:0.3%,n:1367	-

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specimen	asm	date	length	genes	frameshifts	is circular	reference
No matching records found

Psoricoptera gibbosella