Tree of Life QC: Species Report

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

NCBI taxon id:	347965
Order:	Hemiptera
Family:	Nabidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Paraneoptera;Hemiptera;Heteroptera;Panheteroptera;Cimicomorpha;Nabidae;Nabinae;Nabis;Nabis;
GoaT genome size (M):	489 (ancestor)
GoaT asm span (M):	533 (ancestor)
GoaT chr no.:	36 (ancestor)
ToLID prefix:	ihNabFeru

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
ihNabFeru1	Ox000307	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA7520441	SAMEA7520355
ihNabFeru2	Ox002001	UNIVERSITY OF OXFORD	NOT_COLLECTED	WHOLE_ORGANISM	SAMEA110451724	SAMEA110451538

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	ihNabFeru1	31	9.692	1,935,737,540	66.38	23.20	96.89	0.47
pacbio	ihNabFeru1	31	37.11	52,473,967	82.61	3.02	89.43	3.61
hic-arima2	ihNabFeru2	31	22.17	1,680,676,662	69.58	5.11	96.75	0.67

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	ihNabFeru1	2021-03-25	80864	m64221e_210325_144012	A01	1016	12,243,822,883	7,013	SAMEA7520441

id	taxon	similarity	seq	country	latitude	longitude
EUBUG210-11	Nabis ferus	0.9969	COI-5P	Germany	53.106	14.018
GBMIN41038-13	Nabis ferus	0.9938	COI-5P	[object Object]	[object Object]	[object Object]
GBMHH29580-19	Nabis ferus	0.9832	COI-5P	China	[object Object]	[object Object]
GBMHH29579-19	Nabis ferus	0.9832	COI-5P	China	[object Object]	[object Object]
EUBUG221-11	Nabis ferus	0.9794	COI-5P	Germany	53.109	14.009
GMBMG309-17	Nabis ferus	0.9733	COI-5P	Belarus	53.9156	27.6062
EUBUG220-11	Nabis ferus	0.9692	COI-5P	Germany	53.109	14.009
FBHET878-12	Nabis ferus	0.9679	COI-5P	Germany	48.1272	11.5464
FBHET877-12	Nabis ferus	0.9664	COI-5P	Austria	48.1268	16.9369
GBMHH29622-19	Nabis sp. 8 XT-2018	0.9205	COI-5P	China	[object Object]	[object Object]

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Chromium genome	ihNabFeru1	2020-03-17	33822_5#7	87,536,696	13,218,041,096	SAMEA7520441	qc complete	Nabis ferus (1.00)
Chromium genome	ihNabFeru1	2020-03-17	33822_5#8	127,292,840	19,221,218,840	SAMEA7520441	qc complete	Nabis ferus (1.00)
Chromium genome	ihNabFeru1	2020-03-17	33822_5#5	78,074,172	11,789,199,972	SAMEA7520441	qc complete	Nabis ferus (1.00)
Chromium genome	ihNabFeru1	2020-03-17	33822_5#6	103,805,098	15,674,569,798	SAMEA7520441	qc complete	Nabis ferus (1.00)
Hi-C - Arima v2	ihNabFeru2	2023-01-09	46359_3#6	759,366,562	114,664,350,862	SAMEA110451724	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
0.977418	[426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...]
0.941819	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.915608	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.914767	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.913621	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.912446	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.908727	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.907748	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.906409	[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.902507	[2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, 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
ihNabFeru1

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

Nabis ferus