Tree of Life QC: Species Report - Sciurus carolinensis

Info

NCBI taxon id:	30640
Order:	Rodentia
Family:	Sciuridae
NCBI lineage:	Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires;Rodentia;Sciuromorpha;Sciuridae;Sciurinae;Sciurini;Neosciurus;
GoaT genome size (M):	4,713 (direct)
GoaT asm span (M):	2,815 (direct)
GoaT chr no.:	40 (direct)
ToLID prefix:	mSciCar

Specimens

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

Loading, please wait

public_name	specimen_id	gal	sex	organism_part	biosample	biospecimen
mSciCar2	SAN0001682	SANGER INSTITUTE	MALE	MUSCLE	SAMEA9362440	SAMEA9362411
mSciCar2	SAN0001682	SANGER INSTITUTE	MALE	HEART	SAMEA9362442	SAMEA9362411
mSciCar2	SAN0001682	SANGER INSTITUTE	MALE	LIVER	SAMEA9362443	SAMEA9362411
mSciCar2	SAN0001682	SANGER INSTITUTE	MALE	TESTIS	SAMEA9362445	SAMEA9362411
mSciCar2	SAN0001682	SANGER INSTITUTE	MALE	SKIN	SAMEA9362441	SAMEA9362411

Showing 1 to 5 of 7 rows

Spectra estimates

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

Loading, please wait

source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
hic-dovetail	mSciCar1	31	58.49	3,388,283,630	0.00	100.00	3.88	0.22
10x	mSciCar1	31	15.51	4,981,670,285	53.95	0.73	98.84	0.65

Sequence data

PacBio run data

Below are stats for each PacBio seqeuncing run collected for this species.

Loading, please wait

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession	run accession
PacBio - CLR	mSciCar1	2018-08-01	63157	m54205_180801_123407	A01	-	8,037,727,500	29,010	SAMEA994726	ERR3313329
PacBio - CLR	mSciCar1	2018-08-02	63190	m54205_180802_122310	A01	-	10,049,979,868	26,282	SAMEA994726	ERR3313331
PacBio - CLR	mSciCar1	2018-08-02	63190	m54205_180802_223847	B01	-	8,963,613,043	28,975	SAMEA994726	ERR3313332
PacBio - CLR	mSciCar1	2018-08-03	63216	m54097_180803_131457	A01	-	10,071,689,542	28,855	SAMEA994726	ERR3313242
PacBio - CLR	mSciCar1	2018-08-04	63216	m54097_180804_095540	G01	-	9,932,636,985	28,015	SAMEA994726	ERR3313243
PacBio - CLR	mSciCar1	2018-08-04	63216	m54097_180804_201334	D01	-	11,553,185,135	27,019	SAMEA994726	ERR3313244
PacBio - CLR	mSciCar1	2018-08-05	63216	m54097_180805_063119	E01	-	8,739,047,135	28,002	SAMEA994726	ERR3313245
PacBio - CLR	mSciCar1	2018-08-06	63216	m54097_180806_030555	C01	-	8,929,787,456	25,570	SAMEA994726	ERR3313247
PacBio - CLR	mSciCar1	2018-08-06	63216	m54097_180806_132257	H01	-	10,506,725,268	26,437	SAMEA994726	ERR3313248
PacBio - CLR	mSciCar1	2018-08-07	63265	m54097_180807_095701	A01	-	4,931,030,084	29,115	SAMEA994726	ERR3313249
PacBio - CLR	mSciCar1	2018-08-08	63329	m54097_180808_161956	A01	-	7,324,281,317	28,805	SAMEA994726	ERR3313250
PacBio - CLR	mSciCar1	2018-08-08	63315	m54205_180808_202926	B01	-	8,537,323,214	28,127	SAMEA994726	ERR3313342
PacBio - CLR	mSciCar1	2018-08-09	63371	m54097_180809_154045	A01	-	10,183,995,684	25,343	SAMEA994726	ERR3313252
PacBio - CLR	mSciCar1	2018-08-09	63329	m54097_180809_022908	B01	-	9,167,114,585	27,929	SAMEA994726	ERR3313251
PacBio - CLR	mSciCar1	2018-08-09	63315	m54205_180809_165916	D01	-	9,787,078,042	27,597	SAMEA994726	ERR3313344
PacBio - CLR	mSciCar1	2018-08-09	63315	m54205_180809_064441	C01	-	8,109,516,764	28,241	SAMEA994726	ERR3313343
PacBio - CLR	mSciCar1	2018-08-10	63390	m54097_180810_151930	A01	-	11,625,820,631	28,559	SAMEA994726	ERR3313253
PacBio - CLR	mSciCar1	2018-08-10	63388	m54205_180810_212317	B01	-	11,897,740,498	25,917	SAMEA994726	ERR3313346
PacBio - CLR	mSciCar1	2018-08-10	63388	m54205_180810_111106	A01	-	10,703,393,326	23,895	SAMEA994726	ERR3313345
PacBio - CLR	mSciCar1	2018-08-11	63390	m54097_180811_114717	C01	-	11,155,520,098	28,445	SAMEA994726	ERR3313255

Showing 1 to 20 of 23 rows rows per page

id	taxon	similarity	seq	country	latitude	longitude

Illumina run data

Illumina run stats.

Loading, please wait

pipeline	specimen	date	run id	read pairs	yield	sample accession	run accession	run status	barcode
Custom	mSciCar1	2019-07-16	30075_3#1	894,727,304	135,103,822,904	SAMEA994726	ERR3850937	qc complete	Sciurus carolinensis (1.00)
Hi-C - Dovetail	mSciCar1	2019-04-04	28852_6#1	860,673,842	129,961,750,142	SAMEA994726	ERR3312500	qc complete	Sciurus carolinensis (1.00)
Hi-C - Dovetail	mSciCar1	2019-04-04	28852_5#1	857,705,462	129,513,524,762	SAMEA994726	ERR3312499	qc complete	Sciurus carolinensis (1.00)
Hi-C - Dovetail	mSciCar1	2019-09-26	30821_2#1	878,665,228	132,678,449,428	SAMEA994726	ERR5528450	qc complete
Chromium genome	mSciCar1	2018-08-24	26530_8#1	208,987,836	31,557,163,236	SAMEA994726	ERR3316173	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-30	26447_3#1	198,422,064	29,961,731,664	SAMEA994726	ERR3316153	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-30	26447_3#2	316,605,820	47,807,478,820	SAMEA994726	ERR3316154	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-30	26447_3#4	177,327,032	26,776,381,832	SAMEA994726	ERR3316156	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-30	26447_3#3	145,148,922	21,917,487,222	SAMEA994726	ERR3316155	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-24	26530_8#4	187,668,428	28,337,932,628	SAMEA994726	ERR3316176	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-24	26530_8#3	152,416,610	23,014,908,110	SAMEA994726	ERR3316175	qc complete	Sciurus carolinensis (1.00)
Chromium genome	mSciCar1	2018-08-24	26530_8#2	334,734,730	50,544,944,230	SAMEA994726	ERR3316174	qc complete	Sciurus carolinensis (1.00)
RNA-seq dUTP eukaryotic	mSciCar2	2021-12-21	42582_1#6	80,027,348	12,084,129,548	SAMEA9362442	ERR8373757	qc complete	Sciurus carolinensis (1.00)
RNA-seq dUTP eukaryotic	mSciCar2	2021-12-21	42582_1#4	91,831,862	13,866,611,162	SAMEA9362443	ERR8373755	qc complete	Sciurus carolinensis (1.00)
RNA-seq dUTP eukaryotic	mSciCar2	2021-12-21	42582_1#2	79,825,232	12,053,610,032	SAMEA9362445	ERR8373753	qc complete	Sciurus carolinensis (1.00)
RNA PolyA	mSciCar2	2022-08-23	45657_1#42	61,095,290	9,225,388,790	SAMEA9362444		qc complete	Sciurus carolinensis (1.00)
RNA-seq dUTP eukaryotic	mSciCar2	2021-12-21	42582_1#5	85,362,452	12,889,730,252	SAMEA9362441	ERR8373756	qc complete	Sciurus carolinensis (1.00)
RNA PolyA	mSciCar2	2022-08-23	45657_1#45	62,746,578	9,474,733,278	SAMEA9362441		qc complete	Sciurus carolinensis (1.00)
RNA PolyA	mSciCar2	2022-08-23	45657_1#46	57,670,176	8,708,196,576	SAMEA9362442		qc complete	Sciurus carolinensis (1.00)
RNA PolyA	mSciCar2	2022-08-23	45657_1#43	50,184,386	7,577,842,286	SAMEA9362443		qc complete	Sciurus carolinensis (1.00)

Showing 1 to 20 of 25 rows rows per page

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
No matching records found

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

Loading, please wait

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

Re-assembly of reads classified under each identified SSU Marker family.

Loading, please wait

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.

Loading, please wait

specimen	visualisation
mSciCar1

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

BTK datasets:

mSciCar1

Assemblies

In-progress assembly QC.

Loading, please wait

specimen	asm	date	contig N50	contigs	scaffold N50	scaffolds	length	BUSCO	merqury
No matching records found

Organelles

In-progress organelle results from MitoHiFi2.

Loading, please wait

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

Sciurus carolinensis

Mash screen

SSU Marker species

SSU Marker re-assembly

Readviz classification

Contigviz classification

BlobToolKit