Tree of Life QC: Species Report

Info

NCBI taxon id:	688445
Order:	Lepidoptera
Family:	Geometridae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Lepidoptera;Glossata;Ditrysia;Geometroidea;Geometridae;Ennominae;Macaria;
GoaT genome size (M):	332 (ancestor)
GoaT asm span (M):	393 (direct)
GoaT chr no.:	60 (ancestor)
ToLID prefix:	ilMacNota

Specimens

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

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public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ilMacNota1	Ox000816	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA7746716	SAMEA7746623
ilMacNota1	Ox000816	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746716	SAMEA7746623
ilMacNota1	Ox000816	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA7746717	SAMEA7746623
ilMacNota2	Ox001924	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA10979626	SAMEA10979187
ilMacNota2	Ox001924	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA10979625	SAMEA10979187

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Spectra estimates

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

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source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)
10x	ilMacNota1	31	52.25	431,214,152	35.03	0.86	95.03	0.37
pacbio	ilMacNota1	31	28.9	391,473,127	26.02	0.80	98.63	0.17
hic-arima2	ilMacNota1	31	64.23	480,577,177	62.72	1.08	97.92	0.42

Sequence data

PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

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pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ilMacNota1	2021-03-21	80708	m64221e_210321_192024	D01	1012	23,910,169,993	14,939	SAMEA7746717	ERR7254658

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id	taxon	similarity	seq	country	latitude	longitude
GBGL10430-12	Macaria notata	1	COI-5P	[object Object]	[object Object]	[object Object]
GWOAL132-09	Macaria notata	1	COI-5P	France	49.182	3.444
GWOAL133-09	Macaria notata	1	COI-5P	France	47.949	2.208
LON5474-16	Macaria notata	1	COI-5P	Norway	58.2395	6.69959
LON057-08	Macaria notata	1	COI-5P	Norway	60.915	12.2731
CGUKA535-09	Macaria notata	1	COI-5P	United Kingdom	51.34	-0.66
GWORM686-09	Macaria notata	1	COI-5P	Germany	48.918	12.9883
GWORE2016-09	Macaria notata	1	COI-5P	Germany	48.2572	11.545
GWORB2943-08	Macaria notata	1	COI-5P	Germany	49.0209	12.2879
GWORL373-09	Macaria notata	1	COI-5P	Germany	48.24	11.5819

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Illumina run data

Illumina run stats.

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pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Chromium genome	ilMacNota1	2021-04-06	37204_1#18	130,262,070	19,669,572,570	SAMEA7746717	ERR7253246	qc complete	Macaria notata (1.00)
Chromium genome	ilMacNota1	2021-04-06	37204_1#17	124,768,242	18,840,004,542	SAMEA7746717	ERR7253245	qc complete	Macaria notata (1.00)
Chromium genome	ilMacNota1	2021-04-06	37204_1#20	65,496,452	9,889,964,252	SAMEA7746717	ERR7253248	qc complete	Macaria notata (1.00)
Chromium genome	ilMacNota1	2021-04-06	37204_1#19	135,615,830	20,477,990,330	SAMEA7746717	ERR7253247	qc complete	Macaria notata (1.00)
Hi-C - Arima v2	ilMacNota1	2021-11-02	41658_2#2	578,987,764	87,427,152,364	SAMEA7746716	ERR7253249	qc complete	Macaria notata (1.00)
RNA PolyA	ilMacNota2	2022-08-23	45657_1#83	58,296,400	8,802,756,400	SAMEA10979625		qc complete	Macaria notata (1.00)

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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
0.922791	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
ilMacNota1	atg000190l	1900	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;

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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
ilMacNota1

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

Assemblies

In-progress assembly QC.

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specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
ilMacNota1	hicanu	2021-10-31	9,818,497	1,293			791,845,139	C:99.1%[S:60.1%,D:39.0%],F:0.4%,M:0.5%,n:1367	Q43.0-C97.9(10X); Q71.3-C99.5(HiFi)
ilMacNota1	hicanu.purging	2021-10-31	12,589,549	71			399,625,527	C:99.0%[S:97.9%,D:1.1%],F:0.4%,M:0.6%,n:1367	Q57.3-C97.8(10X); Q75.5-C99.5(HiFi)
ilMacNota1	hifiasm.purging	2021-10-31	13,783,241	34			393,811,849	C:99.1%[S:98.2%,D:0.9%],F:0.4%,M:0.5%,n:1367	Q60.9-C97.8(10X); Q66.1-C99.5(HiFi)
ilMacNota1	hifiasm.scaff.salsa	2021-10-31	13,783,192	34			393,810,829		-
ilMacNota1	hifiasm.scaff.yahs	2021-10-31	13,783,192	34	13,783,192	33	393,811,029		-
ilMacNota1	hifiasm	2021-10-31	13,783,241	72			403,251,098	C:99.1%[S:97.7%,D:1.4%],F:0.4%,M:0.5%,n:1367	Q58.1-C97.8(10X); Q65.6-C99.5(HiFi)

Organelles

In-progress organelle results from MitoHiFi2.

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specimen	asm	date	length	genes	frameshifts	reference
ilMacNota1	hicanu	2021-10-31	15,583	36	None	NC_057638.1; 15,538 bp; 37 genes
ilMacNota1	reads	2021-10-31	15,416	36	CYTB;ND5	NC_057638.1; 15,538 bp; 37 genes
ilMacNota1	hifiasm	2021-10-31	15,407	36	None	NC_057638.1; 15,538 bp; 37 genes

Macaria notata

Mash screen

SSU Marker species

SSU Marker re-assembly

Readviz classification

Contigviz classification