Tree of Life QC: Species Report - Cistogaster globosa

NCBI taxon id:	1918221 NCBI; ENA; GoaT
Order:	Diptera
Family:	Tachinidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Oestroidea;Tachinidae;Phasiinae;Phasiini;Cistogaster;
GoaT genome size (M):	691 (ancestor)
GoaT asm span (M):	837 (direct)
GoaT chr no.:	12 (ancestor)
GoaT haploid no.:	6 (ancestor)
GoaT ploidy:	3 (ancestor)
ToLID prefix:	idCisGlob

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
idCisGlob1	Ox000765	UNIVERSITY OF OXFORD	MALE	WHOLE_ORGANISM	SAMEA7746574	SAMEA7746478
idCisGlob2	Ox001751	UNIVERSITY OF OXFORD	MALE	WHOLE_ORGANISM	SAMEA10979401	SAMEA10979013
idCisGlob3	NHMUK014036993	NATURAL HISTORY MUSEUM	NOT_PROVIDED	HEAD	SAMEA112221931	SAMEA112221836
idCisGlob3	NHMUK014036993	NATURAL HISTORY MUSEUM	NOT_PROVIDED	ABDOMEN	SAMEA112222070	SAMEA112221836
idCisGlob3	NHMUK014036993	NATURAL HISTORY MUSEUM	NOT_PROVIDED	THORAX	SAMEA112221936	SAMEA112221836

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
10x	idCisGlob1	31	25.98	1,033,690,658	63.58	3.42	98.05	0.45	histogram.txt
pacbio	idCisGlob1	31	26.95	793,267,946	42.50	3.34	94.83	0.20	histogram.txt
hic-arima2	idCisGlob2	31	41.85	1,080,411,168	0.00	100.00	3.48	0.17	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession
PacBio - HiFi	idCisGlob1	2021-03-29	80884	m64228e_210329_153943	D01	1018	15,310,707,049	13,509	SAMEA7746574	ERR9127946
PacBio - HiFi	idCisGlob1	2021-04-26	81637	m64221e_210426_130254	D01	1018	7,178,652,825	14,065	SAMEA7746574	ERR9127945
PacBio - HiFi (ULI)	idCisGlob1	2022-03-18	TRACTION-RUN-77	m64094e_220318_145339	A01	-	23,163,075,559	8,858	SAMEA7746574

id	taxon	similarity	seq	country	latitude	longitude
TACFI760-13	Cistogaster globosa	0.9985	COI-5P	Germany	[object Object]	[object Object]
TACFI444-12	Cistogaster globosa	0.9985	COI-5P	Finland	61.548	23.943
FIDIP2726-12	Cistogaster globosa	0.9985	COI-5P	Finland	60.221	24.857
TACHF095-19	Cistogaster globosa	1	COI-5P	Netherlands	[object Object]	[object Object]
NOBRA337-15	Diptera	1	COI-5P	Norway	58.346	8.534
FIDIP492-11	Cistogaster globosa	0.9954	COI-5P	Finland	59.932	22.413
CNCDT044-12	Diptera	0.9938	COI-5P	Czech Republic	50.1167	14.35
CNCDT043-12	Diptera	0.9908	COI-5P	Poland	[object Object]	[object Object]
NOBRA338-15	Diptera	0.9908	COI-5P	Norway	59.033	11.009
TACHF040-19	Cistogaster globosa	0.9908	COI-5P	Bulgaria	43.1025	23.4433

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
Chromium genome	idCisGlob1	2021-05-25	37883_1#18	112,435,776	16,977,802,176	SAMEA7746574		qc complete	Cistogaster globosa (1.00)
Chromium genome	idCisGlob1	2021-05-25	37883_1#19	132,082,724	19,944,491,324	SAMEA7746574		qc complete	Cistogaster globosa (1.00)
Chromium genome	idCisGlob1	2021-05-25	37883_1#17	137,915,984	20,825,313,584	SAMEA7746574		qc complete	Cistogaster globosa (1.00)
Chromium genome	idCisGlob1	2021-05-25	37883_1#20	178,059,996	26,887,059,396	SAMEA7746574		qc complete	Cistogaster globosa (1.00)
Hi-C - Arima v2	idCisGlob2	2022-02-09	43500_3#3	788,255,266	119,026,545,166	SAMEA10979401	ERR9123839	qc complete	Cistogaster globosa (1.00)
RNA PolyA	idCisGlob3	2024-03-15	48593_1#1	59,040,880	8,915,172,880	SAMEA112222070		qc complete

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
0.947887	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.94428	[77 seqs] NZ_JXKS01000001.1 Enterococcus haemoperoxidus strain DSM 15920 Scaffold1, whole genome shotgun sequence [...]
0.934669	[35 seqs] NZ_BAKW01000035.1 Asaia platycodi JCM 25414 DNA, contig: JCM25414.contig00035, whole genome shotgun sequence [...]
0.922553	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.918304	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.917245	[90 seqs] NZ_JWAW01000005.1 Enterococcus faecalis strain 116_EFLS 151_15451_520908, whole genome shotgun sequence [...]
0.916433	[2017 seqs] NW_004087753.1 Ichthyophthirius multifiliis unplaced genomic scaffold scaff_1120509249386, whole genome shotgun sequence [...]
0.914767	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.914198	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.91333	[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 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
idCisGlob1

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

idCisGlob1.hifiasm.20220217

BTK datasets:

idCisGlob1Hap idCisGlob1Pri

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
idCisGlob1	hicanu.purging	2022-02-12	1,855,446	3,052			892,781,461	C:99.4%[S:97.9%,D:1.5%],F:0.1%,M:0.5%,n:1367	Q48.4-C92.9(10X); Q65.6-C95.9(HiFi)
idCisGlob1	hicanu	2022-02-12	1,110,132	10,599			1,900,538,892	C:99.8%[S:4.0%,D:95.8%],F:0.1%,M:0.1%,n:1367	Q45.8-C95.9(10X); Q65.6-C99.1(HiFi)
idCisGlob1	hifiasm.purging	2022-02-17	4,079,316	1,287			840,222,375	C:99.4%[S:98.7%,D:0.7%],F:0.1%,M:0.5%,n:1367	Q59.1-C95.9(HiFi)
idCisGlob1	hifiasm.scaff.salsa	2022-02-17	3,986,424	1,307	12,124,818	1,113	840,319,375		-
idCisGlob1	hifiasm.scaff.yahs	2022-02-17	4,072,864	1,384	122,477,086	1,079	840,283,375		-
idCisGlob1	hifiasm	2022-02-17	2,757,908	2,405			1,042,082,364	C:99.4%[S:95.6%,D:3.8%],F:0.1%,M:0.5%,n:1367	Q58.1-C99.1(HiFi)
idCisGlob1	hifiasm.scaffolding.salsa	2022-02-17	3,986,424	1,307	12,124,818	1,113	840,319,375	C:99.5%[S:98.7%,D:0.8%],F:0.1%,M:0.4%,n:1367	Q59.1-C95.9(HiFi)
idCisGlob1	hifiasm.scaffolding.yahs	2022-02-17	4,072,864	1,384	122,477,086	1,079	840,283,375	C:99.4%[S:98.7%,D:0.7%],F:0.1%,M:0.5%,n:1367	Q59.1-C95.9(HiFi)

specimen	asm	organelle	date	length	genes	frameshifts	seqs	reference
idCisGlob1	mitohifi.hicanu	mito	2022-02-12	69,462	10	None	1	NC_050938.1; 15,792 bp; 37 genes
idCisGlob1	mitohifi.reads	mito	2022-02-12	50,100	59	None	1	NC_050938.1; 15,792 bp; 37 genes
idCisGlob1	mitohifi.hifiasm	mito	2022-02-17	16,968	37	None	1	NC_050938.1; 15,792 bp; 37 genes

Cistogaster globosa

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

idCisGlob1.hifiasm.20220217

Assemblies

Organelles

Cistogaster globosa

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification

idCisGlob1.hifiasm.20220217

BlobToolKit