Tree of Life QC: Species Report - Selenia tetralunaria

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

NCBI taxon id:	934895
Order:	Lepidoptera
Family:	Geometridae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Selenia;
GoaT genome size (M):	831 (ancestor)
GoaT asm span (M):	1,030 (ancestor)
GoaT chr no.:	58 (direct)
ToLID prefix:	ilSelTetr

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilSelTetr1	Ox000607	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA7701644	SAMEA7701471
ilSelTetr1	Ox000607	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA7701643	SAMEA7701471
ilSelTetr1	Ox000607	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7701643	SAMEA7701471

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 (%)
10x	ilSelTetr1	31	16.59	1,106,672,055	42.67	0.87	99.41	0.45
pacbio	ilSelTetr1	31	41.16	27,315,001	86.81	3.39	88.95	4.11
hic-arima2	ilSelTetr1	31	66.74	664,723,390	0.00	100.00	5.48	0.11

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilSelTetr1	2021-05-14	82303	m64221e_210514_185712	B01	1010	8,285,454,611	8,932	SAMEA7701644

id	taxon	similarity	seq	country	latitude	longitude
GWOR4455-09	Selenia tetralunaria	0.9985	COI-5P	Austria	47.725	13.599
LON5432-16	Selenia tetralunaria	0.9985	COI-5P	Norway	58.1611	8.09929
CGUKA613-09	Selenia tetralunaria	0.9985	COI-5P	United Kingdom	54.19	-2.8
CGUKA813-09	Selenia tetralunaria	0.9985	COI-5P	United Kingdom	[object Object]	[object Object]
GWOSI019-10	Selenia tetralunaria	0.9985	COI-5P	Croatia	44.8	15.7167
LEFIE166-10	Selenia tetralunaria	0.9985	COI-5P	Finland	67.276	23.753
LEFIF206-10	Selenia tetralunaria	0.9985	COI-5P	Finland	59.836	23.236
LEFIA234-10	Selenia tetralunaria	0.9985	COI-5P	Finland	61.108	28.799
LENOA1070-11	Selenia tetralunaria	0.9985	COI-5P	France	49.547	1.56
PHLAV024-12	Selenia tetralunaria	0.9985	COI-5P	Austria	47.267	9.667

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Chromium genome	ilSelTetr1	2021-05-26	38128_3#18	99,263,490	14,988,786,990	SAMEA7701644	qc complete
Chromium genome	ilSelTetr1	2021-05-26	38128_3#19	99,035,578	14,954,372,278	SAMEA7701644	qc complete	Selenia tetralunaria (1.00)
Chromium genome	ilSelTetr1	2021-05-26	38128_3#17	97,380,008	14,704,381,208	SAMEA7701644	qc complete
Chromium genome	ilSelTetr1	2021-05-26	38128_3#20	86,748,982	13,099,096,282	SAMEA7701644	qc complete	Selenia tetralunaria (1.00)
Hi-C - Arima v2	ilSelTetr1	2021-05-16	37941_1#3	752,905,658	113,688,754,358	SAMEA7701643	qc complete	Selenia tetralunaria (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
0.915885	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
ilSelTetr1

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
No matching records found

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

Selenia tetralunaria