Tree of Life QC: Species Report - Perforatus perforatus

NCBI taxon id:	1562161 NCBI; ENA; GoaT
Order:	Sessilia
Family:	Balanidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Crustacea;Multicrustacea;Cirripedia;Thoracica;Thoracicalcarea;Balanomorpha;Balanoidea;Balanidae;Concavinae;Perforatus;
GoaT genome size (M):	1,139 (ancestor)
GoaT asm span (M):	572 (ancestor)
GoaT chr no.:	16 (ancestor)
GoaT haploid no.:	8 (ancestor)
GoaT ploidy:	6 (ancestor)
ToLID prefix:	qxPerPerf

Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).

tolid	specimen_id	gal	sex	organism_part	biosample	biospecimen
qxPerPerf1	MBA-201115-005A	MARINE BIOLOGICAL ASSOCIATION	NOT_COLLECTED	ANTERIOR_BODY	SAMEA8724846	SAMEA8724782
qxPerPerf2	MBA-201115-005B	MARINE BIOLOGICAL ASSOCIATION	NOT_COLLECTED	ANTERIOR_BODY	SAMEA8724847	SAMEA8724783
qxPerPerf3	MBA-201115-005C	MARINE BIOLOGICAL ASSOCIATION	NOT_COLLECTED	ANTERIOR_BODY	SAMEA110451073	SAMEA110450151
qxPerPerf3	MBA-201115-005C	MARINE BIOLOGICAL ASSOCIATION	NOT_COLLECTED	POSTERIOR_BODY	SAMEA110451072	SAMEA110450151
qxPerPerf4	MBA-201115-005D	MARINE BIOLOGICAL ASSOCIATION	NOT_COLLECTED	POSTERIOR_BODY	SAMEA110451074	SAMEA110450152

Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
hic-arima2	qxPerPerf6	31	39.38	1,057,373,311	0.00	100.00	1.16	0.33	histogram.txt
pacbio	qxPerPerf5	31	17.3	365,174,251	66.54	18.39	78.09	1.10	histogram.txt
pacbio	qxPerPerf2	31	38.62	52,549,285	85.56	2.87	88.20	2.90	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	qxPerPerf2	2021-06-24	83727	m64222e_210624_170357	A01	1018	10,130,002,453	12,576	SAMEA8724847
PacBio - HiFi	qxPerPerf5	2023-10-16	TRACTION-RUN-884	m64222e_231016_000732	D01	2006	17,871,973,182	10,277	SAMEA110451077

id	taxon	similarity	seq	country	latitude	longitude
GBCX6744-17	Perforatus perforatus	0.9977	COI-5P	Guam	13.4454	144.78
GBMNC67155-20	Perforatus perforatus	0.9975	COI-5P	Spain	[object Object]	[object Object]
GBCRO4446-19	Perforatus perforatus	0.9975	COI-5P	Spain	40.365	-3.65163
GBCX7289-17	Perforatus perforatus	0.9952	COI-5P	[object Object]	[object Object]	[object Object]
GBCX2078-14	Amphibalanus variegatus	0.895	COI-5P	[object Object]	[object Object]	[object Object]
GBCX2079-14	Amphibalanus variegatus	0.895	COI-5P	[object Object]	[object Object]	[object Object]
GBA10752-13	Amphibalanus variegatus	0.8904	COI-5P	[object Object]	[object Object]	[object Object]
GBA10753-13	Amphibalanus variegatus	0.8904	COI-5P	[object Object]	[object Object]	[object Object]
GBMNC71382-20	Amphibalanus variegatus	0.8904	COI-5P	Indonesia	[object Object]	[object Object]
GBMNC71381-20	Amphibalanus variegatus	0.8881	COI-5P	Indonesia	[object Object]	[object Object]

pipeline	specimen	date	run id	flowcell	type	yield	N50	sample accession	report
No matching records found

Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Hi-C - Arima v2	qxPerPerf6	2023-06-13	47432_1#1	763,171,212	115,238,853,012	SAMEA110451078		qc complete	Perforatus perforatus (1.00)

Cobionts

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
0.919595	[118 seqs] NZ_AJYG02000001.1 Enterovibrio calviensis 1F-211 1F-211_contig_0, whole genome shotgun sequence [...]
0.916976	[162 seqs] NZ_MAKF01000001.1 Vibrio splendidus strain 13B01 13B01_contig_0, whole genome shotgun sequence [...]
0.911545	[93 seqs] NZ_LNGM01000001.1 Photobacterium sanguinicancri strain ME15 contig00001, whole genome shotgun sequence [...]
0.910625	[282 seqs] NZ_AJZK01000001.1 Vibrio splendidus 0407ZC148 subcontig_1, whole genome shotgun sequence [...]

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Species composition by small subunit (SSU) presence in the assembly with MarkerScan.

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specimen	contig	SSU length	attributed taxonomy by SSU
No matching records found

MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.

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specimen	family	classified reads			original assembly				re-assembly
specimen	family	count	(%)	BUSCO	BUSCO	contigs	contig length	number of reads	BUSCO	contigs	contig length	number of reads
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
qxPerPerf2

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

Perforatus perforatus

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

Assemblies

Organelles

Perforatus perforatus

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification