Tree of Life QC: Species Report - Planorbis planorbis

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

NCBI taxon id:	191805
Order:	Hygrophila
Family:	Planorbidae
NCBI lineage:	Eukaryota;Metazoa;Spiralia;Lophotrochozoa;Mollusca;Gastropoda;Heterobranchia;Euthyneura;Panpulmonata;Hygrophila;Lymnaeoidea;Planorbidae;Planorbis;
GoaT genome size (M):	1,398 (direct)
GoaT asm span (M):	1,069 (ancestor)
GoaT chr no.:	48 (ancestor)
ToLID prefix:	xgPlaPlan

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
xgPlaPlan1	NHMUK014361595	NATURAL HISTORY MUSEUM	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7521413	SAMEA7521336

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	xgPlaPlan1	31	18.29	933,122,300	70.68	14.48	86.77	0.95
pacbio	xgPlaPlan1	31	35.01	466,357	68.60	2.46	88.68	5.29
hic-arima2	xgPlaPlan1	31	38.93	1,244,857,885	38.03	0.54	94.60	0.44

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	xgPlaPlan1	2020-10-17	77750	m64089_201017_174048	D01	1003	177,048,863	5,503	SAMEA7521413

id	taxon	similarity	seq	country	latitude	longitude
GBML34830-19	Planorbis planorbis	0.9118	COI-5P	Russia	[object Object]	[object Object]
GBML34733-19	Planorbis planorbis	0.9092	COI-5P	Poland	[object Object]	[object Object]
GBMLG0718-06	Planorbis sp. EAR-2003	0.9085	COI-5P	Ukraine	[object Object]	[object Object]
GBML29471-19	Planorbis sp. 1 MFH-2015	0.9068	COI-5P	Iran	[object Object]	[object Object]
GBMIN109262-17	Planorbis planorbis	0.9048	COI-5P	Austria	[object Object]	[object Object]
GBMIN109261-17	Planorbis sp. 2 MFH-2015	0.9021	COI-5P	Iran	[object Object]	[object Object]
GBMLG7742-09	Planorbis planorbis	0.8997	COI-5P	Germany	[object Object]	[object Object]
GBMLG2741-06	Choanomphalus mongolicus	0.874	COI-5P	[object Object]	[object Object]	[object Object]
GBMLG17202-14	Gyraulus sp.	0.8737	COI-5P	Nepal	27.6494	85.2831
GBMLG17199-14	Gyraulus sp.	0.8725	COI-5P	Nepal	27.5969	85.3791

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status
Chromium genome	xgPlaPlan1	2020-11-09	35346_1#6	127,664,548	19,277,346,748	SAMEA7521413	qc complete
Chromium genome	xgPlaPlan1	2020-11-09	35346_1#8	48,722,532	7,357,102,332	SAMEA7521413	qc complete
Chromium genome	xgPlaPlan1	2020-11-09	35346_1#7	138,040,860	20,844,169,860	SAMEA7521413	qc complete
Chromium genome	xgPlaPlan1	2020-11-09	35346_1#5	102,961,324	15,547,159,924	SAMEA7521413	qc complete
Hi-C - Arima v2	xgPlaPlan1	2020-10-20	35218_6#1	917,983,972	138,615,579,772	SAMEA7521413	qc complete

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
No matching records found

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
xgPlaPlan1

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

Planorbis planorbis