Tree of Life QC: Species Report - Otiorhynchus sulcatus

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

NCBI taxon id:	122849
Order:	Coleoptera
Family:	Curculionidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Coleoptera;Polyphaga;Cucujiformia;Curculionidae;Entiminae;Otiorhynchini;Otiorhynchus;
GoaT genome size (M):	3,246 (ancestor)
GoaT asm span (M):	1,382 (ancestor)
GoaT chr no.:	33 (direct)
ToLID prefix:	icOtiSulc

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
icOtiSulc1	Ox000803	UNIVERSITY OF OXFORD	NOT_COLLECTED	ABDOMEN	SAMEA7746695	SAMEA7746610
icOtiSulc1	Ox000803	UNIVERSITY OF OXFORD	NOT_COLLECTED	THORAX	SAMEA7746694	SAMEA7746610
icOtiSulc1	Ox000803	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746694	SAMEA7746610

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	icOtiSulc1	31	20.65	2,687,781,420	101.88	3.71	94.36	0.26
pacbio	icOtiSulc1	31	12.37	1,654,001,386	54.69	1.83	94.90	0.31
hic-arima2	icOtiSulc1	31	84.01	2,211,770,551	84.09	3.58	96.25	0.29

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	icOtiSulc1	2021-03-13	80528	m64221e_210313_122644	B01	1012	20,496,423,223	13,475	SAMEA7746695
PacBio - HiFi	icOtiSulc1	2021-03-18	80685	m64097e_210318_144326	A01	1012	24,635,862,954	11,909	SAMEA7746695

id	taxon	similarity	seq	country	latitude	longitude
GBCL47545-19	Otiorhynchus sulcatus	0.9988	COI-3P	[object Object]	[object Object]	[object Object]
GBCL47545-19	Otiorhynchus sulcatus	0.9988	COI-3P	[object Object]	[object Object]	[object Object]
GBCL47545-19	Otiorhynchus sulcatus	0.9963	COI-3P	[object Object]	[object Object]	[object Object]
GBCL47545-19	Otiorhynchus sulcatus	0.9963	COI-3P	[object Object]	[object Object]	[object Object]
GBCOG174-13	Otiorhynchus sulcatus	0.9939	COI-5P	[object Object]	[object Object]	[object Object]
GCOL1239-16	Otiorhynchus sulcatus	0.9939	COI-5P	[object Object]	[object Object]	[object Object]
GCOL2334-16	Otiorhynchus sulcatus	0.9939	COI-5P	[object Object]	[object Object]	[object Object]
GCOL3865-16	Otiorhynchus sulcatus	0.9939	COI-5P	[object Object]	[object Object]	[object Object]
GCOL4543-16	Otiorhynchus sulcatus	0.9939	COI-5P	[object Object]	[object Object]	[object Object]
GBCOG174-13	Otiorhynchus sulcatus	0.9924	COI-5P	[object Object]	[object Object]	[object Object]

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Chromium genome	icOtiSulc1	2021-04-08	37177_3#20	217,061,632	32,776,306,432	SAMEA7746695	qc complete	Otiorhynchus sulcatus (1.00)
Chromium genome	icOtiSulc1	2021-04-08	37177_3#19	352,407,830	53,213,582,330	SAMEA7746695	qc complete	Otiorhynchus sulcatus (1.00)
Chromium genome	icOtiSulc1	2021-04-08	37177_3#17	277,270,638	41,867,866,338	SAMEA7746695	qc complete	Otiorhynchus sulcatus (1.00)
Chromium genome	icOtiSulc1	2021-04-08	37177_3#18	248,211,906	37,479,997,806	SAMEA7746695	qc complete	Otiorhynchus sulcatus (1.00)
Hi-C - Arima v2	icOtiSulc1	2021-03-26	36940_2#1	3,353,656,830	506,402,181,330	SAMEA7746694	qc complete	Otiorhynchus sulcatus (1.00)

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
0.945611	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.916433	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.914483	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]
0.913038	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.911847	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.91124	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.909686	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.902876	[2 seqs] NC_004344.2 Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis DNA, complete genome [...]
0.902876	NC_015662.1 Buchnera aphidicola (Cinara tujafilina), complete genome
0.902507	[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, 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
icOtiSulc1

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

Otiorhynchus sulcatus