Tree of Life QC: Species Report - Sapromyzosoma quadripunctata

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

NCBI taxon id:	1825021
Order:	Diptera
Family:	Lauxaniidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Lauxanioidea;Lauxaniidae;Sapromyzosoma;
GoaT genome size (M):	260 (ancestor)
GoaT asm span (M):	398 (ancestor)
GoaT chr no.:	12 (ancestor)
ToLID prefix:	idSapQuap

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
idSapQuap1	Ox000800	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7746691	SAMEA7746607

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	idSapQuap1	31	22.54	896,380,042	56.99	2.95	97.77	0.62
pacbio	idSapQuap1	31	12.21	857,170,346	49.60	2.87	95.98	0.33

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	idSapQuap1	2021-04-01	81048	m64094e_210401_141920	A01	1008	23,248,095,347	15,616	SAMEA7746691

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status
Chromium genome	idSapQuap1	2021-06-01	37642_4#39	123,542,932	18,654,982,732	SAMEA7746691	qc complete
Chromium genome	idSapQuap1	2021-06-01	37642_4#38	122,605,930	18,513,495,430	SAMEA7746691	qc complete
Chromium genome	idSapQuap1	2021-06-01	37642_4#40	100,202,144	15,130,523,744	SAMEA7746691	qc complete
Chromium genome	idSapQuap1	2021-06-01	37642_4#37	100,589,726	15,189,048,626	SAMEA7746691	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
0.940376	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.917512	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.912446	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.911545	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.908403	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.908403	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.903242	[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.900615	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]

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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
idSapQuap1

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

Sapromyzosoma quadripunctata