Tree of Life QC: Species Report - Eupeodes latifasciatus

NCBI taxon id:	1124558 NCBI; ENA; GoaT
Order:	Diptera
Family:	Syrphidae
NCBI lineage:	Eukaryota;Metazoa;Ecdysozoa;Arthropoda;Hexapoda;Insecta;Pterygota;Neoptera;Endopterygota;Diptera;Brachycera;Muscomorpha;Syrphoidea;Syrphidae;Syrphinae;Syrphini;Eupeodes;Eupeodes;
GoaT genome size (M):	528 (ancestor)
GoaT asm span (M):	846 (direct)
GoaT chr no.:	8 (ancestor)
GoaT haploid no.:	4 (ancestor)
GoaT ploidy:	3 (ancestor)
ToLID prefix:	idEupLati

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
idEupLati1	Ox000878	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746843	SAMEA7746776
idEupLati1	Ox000878	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746843	SAMEA7746776
idEupLati1	Ox000878	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746843	SAMEA7746776
idEupLati1	Ox000878	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746843	SAMEA7746776
idEupLati1	Ox000878	UNIVERSITY OF OXFORD	NOT_COLLECTED	HEAD	SAMEA7746843	SAMEA7746776

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
pacbio	idEupLati1	31	13.47	838,903,742	52.08	1.77	97.35	0.18	histogram.txt
10x	idEupLati1	31	23.66	984,352,866	62.33	2.04	98.53	0.42	histogram.txt
hic-arima2	idEupLati1	31	35.01	809,634,658	73.46	5.77	98.46	0.48	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession	barcode
PacBio - HiFi	idEupLati1	2021-05-08	82080	m64222e_210508_202107	B01	1018	18,335,802,352	14,750	SAMEA7746844
PacBio - HiFi	idEupLati1	2021-07-19	84529	m64221e_210719_211234	D01	1018	5,601,325,342	12,565	SAMEA7746844

id	taxon	similarity	seq	country	latitude	longitude
GBMNB24922-20	Eupeodes latifasciatus	0.9969	COI-5P	[object Object]	[object Object]	[object Object]
FIDIP035-11	Eupeodes latifasciatus	0.9969	COI-5P	Finland	61.91	27.29
FIDIP397-11	Eupeodes latifasciatus	0.9969	COI-5P	Finland	64.48	28.168
FIDIP117-11	Eupeodes latifasciatus	0.9969	COI-5P	Finland	60.615	21.929
FIDIP965-12	Eupeodes latifasciatus	0.9969	COI-5P	Finland	60.66	25.682
NORSY258-12	Eupeodes latifasciatus	0.9969	COI-5P	Norway	59.8908	12.162
GMGMT1606-20	Eupeodes latifasciatus	0.9969	COI-5P	Germany	48.165	11.485
GMGMJ696-14	Eupeodes latifasciatus	0.9967	COI-5P	Germany	50.552	7.17
BEEEE369-16	Eupeodes latifasciatus	0.9966	COI-5P	United Kingdom	53.595	-1.563
AMTPD4516-16	Eupeodes latifasciatus	0.9966	COI-5P	Germany	47.3884	10.3444

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 status	barcode
Chromium genome	idEupLati1	2021-03-24	36973_4#24	152,781,172	23,069,956,972	SAMEA7746844	qc complete	Eupeodes latifasciatus (1.00)
Chromium genome	idEupLati1	2021-03-24	36973_4#23	47,091,080	7,110,753,080	SAMEA7746844	qc complete	Eupeodes latifasciatus (1.00)
Chromium genome	idEupLati1	2021-03-24	36973_4#21	168,056,368	25,376,511,568	SAMEA7746844	qc complete	Eupeodes latifasciatus (1.00)
Chromium genome	idEupLati1	2021-03-24	36973_4#22	114,134,000	17,234,234,000	SAMEA7746844	qc complete	Eupeodes latifasciatus (1.00)
Hi-C - Arima v2	idEupLati1	2021-03-26	36940_4#4	544,265,132	82,184,034,932	SAMEA7746843	qc complete	Eupeodes latifasciatus (1.00)
RNA PolyA	idEupLati2	2025-06-09	50494_4#61	120,932,164	18,260,756,764	SAMEA11025346	qc complete
RNA PolyA	idEupLati1	2022-03-25	44268_5#12	31,997,780	4,831,664,780	SAMEA7746845	qc complete	Eupeodes latifasciatus (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.

Loading, please wait

identity	info
0.994253	[120 seqs] NZ_JYPC01000001.1 Wolbachia endosymbiont of Operophtera brumata strain Ob_Wba WbOb01_Sc001, whole genome shotgun sequence [...]
0.921831	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.91391	[426 seqs] NZ_AERW01000001.1 Wolbachia endosymbiont wVitB of Nasonia vitripennis Contig_0001, whole genome shotgun sequence [...]
0.907083	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.906067	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.903242	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.902135	NC_011047.1 Candidatus Phytoplasma mali strain AT complete chromosome
0.900615	NC_010981.1 Wolbachia endosymbiont of Culex quinquefasciatus Pel strain wPip complete genome
0.900227	[3 seqs] NZ_LN890285.1 Buchnera aphidicola (Tuberolachnus salignus) strain BTs genome assembly, chromosome: 1 [...]

Showing 1 to 9 of 9 rows

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

Loading, please wait

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.

Loading, please wait

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.

Loading, please wait

specimen	visualisation
idEupLati1

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
idEupLati1	hifiasm.purging	2021-07-23	2,836,493	1,212			857,068,578		-
idEupLati1	hifiasm.scaff.yahs	2021-07-23	2,785,076	1,255	150,375,976	772	857,155,891		-
idEupLati1	hifiasm.scaff.salsa	2021-07-23	2,740,560	1,243	35,253,144	722	857,319,791		-
idEupLati1	hicanu.purging	2021-07-22	2,327,201	1,684			865,173,652	C:98.9%[S:97.1%,D:1.8%],F:0.3%,M:0.8%,n:1367	Q53.0-C93.9(10X)
idEupLati1	hicanu	2021-07-22	1,590,134	7,814			1,718,878,823	C:99.0%[S:49.7%,D:49.3%],F:0.2%,M:0.8%,n:1367	Q45.4-C94.1(10X)
idEupLati1	hifiasm	2021-07-22	5,426,802	1,628			896,746,934	C:98.5%[S:96.6%,D:1.9%],F:0.3%,M:1.2%,n:1367	Q50.0-C94.0(10X)
idEupLati1	hifiasm.purging_e	2021-07-22	5,614,885	896	5,817,203	868	836,393,855		-
idEupLati1	hifiasm.purging	2021-07-22	5,817,203	869			838,382,277	C:98.5%[S:97.1%,D:1.4%],F:0.3%,M:1.2%,n:1367	Q52.2-C93.7(10X)

Eupeodes latifasciatus

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

Assemblies

Organelles

Eupeodes latifasciatus

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification