Tree of Life QC: Species Report

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

NCBI taxon id:	9860
Order:	Artiodactyla
Family:	Cervidae
NCBI lineage:	Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Laurasiatheria;Artiodactyla;Ruminantia;Pecora;Cervidae;Cervinae;Cervus;
GoaT genome size (M):	3,168 (ancestor)
GoaT asm span (M):	2,895 (direct)
GoaT chr no.:	68 (direct)
ToLID prefix:	mCerEla

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
mCerEla1	SAN0000996	SANGER INSTITUTE	FEMALE	BLOOD	SAMEA7523620	SAMEA7523520
mCerEla1	SAN0000996	SANGER INSTITUTE	FEMALE	BLOOD	SAMEA7523614	SAMEA7523520
mCerEla1	SAN0000996	SANGER INSTITUTE	FEMALE	BLOOD	SAMEA7523618	SAMEA7523520
mCerEla1	SAN0000996	SANGER INSTITUTE	FEMALE	BLOOD	SAMEA7523613	SAMEA7523520
mCerEla1	SAN0000996	SANGER INSTITUTE	FEMALE	BLOOD	SAMEA7523617	SAMEA7523520

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	mCerEla1	31	11.32	3,250,519,959	34.89	0.29	99.43	0.48
pacbio	mCerEla1	31	14.84	3,019,651,561	29.74	0.31	99.29	0.19
hic-arima2	mCerEla1	31	61.06	2,531,337,280	33.72	1.29	97.89	0.58

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession
PacBio - HiFi	mCerEla1	2020-09-11	TRACTION-RUN-47	m64016_200911_163100	B01	1020	21,747,238,671	14,864	SAMEA7523613	ERR6406211
PacBio - HiFi	mCerEla1	2020-09-18	TRACTION-RUN-50	m64089_200918_152723	B01	1020	25,170,380,015	16,022	SAMEA7523613	ERR6406212
PacBio - HiFi	mCerEla1	2020-09-19	TRACTION-RUN-50	m64089_200919_155532	C01	1020	25,345,358,104	15,488	SAMEA7523613	ERR6406213
PacBio - HiFi	mCerEla1	2020-10-08	TRACTION-RUN-56	m64125_201008_110302	A01	1020	23,028,450,952	15,672	SAMEA7523613	ERR6436379

id	taxon	similarity	seq	country	latitude	longitude
GBMIN43643-14	Cervus elaphus	0.9967	COI-5P	[object Object]	[object Object]	[object Object]
GBMIN43639-14	Cervus elaphus	0.9967	COI-5P	[object Object]	[object Object]	[object Object]
GBMIN43635-14	Cervus elaphus	0.9967	COI-5P	[object Object]	[object Object]	[object Object]
GBMIN43632-14	Cervus elaphus	0.9967	COI-5P	[object Object]	[object Object]	[object Object]
GBMA26331-19	Cervus elaphus	0.9951	COI-5P	Denmark	[object Object]	[object Object]
GBMTG716-16	Cervus elaphus	0.9951	COI-5P	[object Object]	[object Object]	[object Object]
GBMNA13656-19	Cervus elaphus	0.9951	COI-5P	New Zealand	[object Object]	[object Object]
GBMIN43638-14	Cervus elaphus	0.995	COI-5P	[object Object]	[object Object]	[object Object]
GBMIN43076-14	Cervus elaphus	0.9934	COI-5P	New Zealand	[object Object]	[object Object]
GBMA26332-19	Cervus elaphus	0.9934	COI-5P	Spain	[object Object]	[object Object]

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Chromium genome	mCerEla1	2020-10-20	35209_6#1	264,578,556	39,951,361,956	SAMEA7523615	ERR6054832	qc complete	Cervus elaphus (1.00)
Chromium genome	mCerEla1	2020-10-20	35209_6#4	217,585,892	32,855,469,692	SAMEA7523615	ERR6054835	qc complete	Cervus elaphus (0.99)
Chromium genome	mCerEla1	2020-10-20	35209_6#3	255,609,822	38,597,083,122	SAMEA7523615	ERR6054834	qc complete	Cervus elaphus yarkandensis (1.00)
Chromium genome	mCerEla1	2020-10-20	35209_6#2	40,467,920	6,110,655,920	SAMEA7523615	ERR6054833	qc complete	Cervus elaphus yarkandensis (1.00)
Hi-C - Arima v2	mCerEla1	2020-11-24	35528_2#2	3,063,297,956	462,557,991,356	SAMEA7523614	ERR6054836	qc complete	Cervus elaphus (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
0.941977	[32 seqs] NC_032650.1 Bos indicus isolate QUIL7308 breed Nelore chromosome 1, Bos_indicus_1.0, whole genome shotgun sequence [...]
0.928167	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.905028	[777 seqs] NC_033646.1 Plasmodium reichenowi strain SY57 chromosome 1, whole genome shotgun sequence [...]
0.903242	[28 seqs] NZ_LTBM01000001.1 Candidatus Phytoplasma oryzae isolate Mbita1 Pmin.contig.0_1, whole genome shotgun sequence [...]
0.903242	[833 seqs] NC_031481.1 Plasmodium gaboni strain SY75 chromosome 1, whole genome shotgun sequence [...]
0.902507	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.901759	NZ_AP013293.1 Candidatus Sulcia muelleri PSPU DNA, complete genome
0.900394	NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete 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
mCerEla1

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
mCerEla1	hifiasm.purging	2020-10-17	63,760,693	317			3,159,819,036	C:95.0%[S:92.6%,D:2.4%],F:2.4%,M:2.6%,n:4104	-
mCerEla1	hifiasm.scaff-sing.salsa	2020-10-17	63,760,408	388	71,624,245	357	3,159,812,217		-
mCerEla1	hifiasm	2020-10-17	63,634,050	535			3,238,811,472	C:95.0%[S:92.6%,D:2.4%],F:2.4%,M:2.6%,n:4104	-
mCerEla1	hicanu.purging	2020-10-17	37,575,104	817			3,236,027,854	C:94.8%[S:92.3%,D:2.5%],F:2.4%,M:2.8%,n:4104	-
mCerEla1	hicanu	2020-10-17	3,777,441	12,668			6,241,657,621	C:94.2%[S:23.4%,D:70.8%],F:2.1%,M:3.7%,n:4104	-

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specimen	asm	date	length	genes	frameshifts	is circular	reference
No matching records found

Cervus elaphus