Tree of Life QC: Species Report - Rhopalus parumpunctatus

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

NCBI taxon id:	1511248
Order:	Hemiptera
Family:	Rhopalidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Heteroptera;Panheteroptera;Pentatomomorpha;Coreoidea;Rhopalidae;Rhopalus;
GoaT genome size (M):	3,237 (ancestor)
GoaT asm span (M):	1,079 (ancestor)
GoaT chr no.:	13 (direct)
ToLID prefix:	ihRhoParu

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ihRhoParu1	Ox000229	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7520449	SAMEA7520361

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
pacbio	ihRhoParu1	31	39.23	90,347,022	90.70	3.00	86.65	2.63

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ihRhoParu1	2020-03-05	TRACTION-RUN-22	m64097_200305_151904	B01	1003	16,217,103,536	19,261	SAMEA7520449

id	taxon	similarity	seq	country	latitude	longitude
GBMHH6786-15	Rhopalus parumpunctatus	1	COI-5P	France	[object Object]	[object Object]
GBMHH6720-15	Rhopalus parumpunctatus	1	COI-5P	France	[object Object]	[object Object]
GBMHH6719-15	Rhopalus parumpunctatus	1	COI-5P	France	[object Object]	[object Object]
GBMHH6787-15	Corizus hyoscyami	0.8914	COI-5P	France	[object Object]	[object Object]
GMGMH004-14	Corizus hyoscyami	0.89	COI-5P	Germany	50.552	7.17
GBMHH19861-19	Corizus sp. HK-2015	0.8831	COI-5P	[object Object]	[object Object]	[object Object]
BBHEM063-09	Harmostes reflexulus	0.8823	COI-5P	United States	30.7743	-101.919
BBHMA978-12	Harmostes reflexulus	0.8823	COI-5P	United States	35.072	-92.545
HCNCS303-09	Harmostes reflexulus	0.8811	COI-5P	Canada	49.0333	-113.9
USHEM286-10	Harmostes reflexulus	0.8811	COI-5P	United States	29.7875	-98.4191

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
No matching records found

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
0.994731	[426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...]
0.946046	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.93163	[198 seqs] NZ_LSYY01000001.1 Wolbachia endosymbiont of Dactylopius coccus strain wDacB Contig_1, whole genome shotgun sequence [...]
0.919849	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.919849	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.917777	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.916433	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.915608	NC_002520.1 Amsacta moorei entomopoxvirus 'L', complete genome
0.914198	[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...]
0.91391	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]

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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
ihRhoParu1

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

Rhopalus parumpunctatus