Tree of Life QC: Species Report

Info

NCBI taxon id:	10116 NCBI; ENA; GoaT
Order:	Rodentia
Family:	Muridae
NCBI lineage:	Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;Mammalia;Eutheria;Euarchontoglires;Glires;Rodentia;Myomorpha;Muroidea;Muridae;Murinae;Rattus;
GoaT genome size (M):	3,198 (direct)
GoaT asm span (M):	2,859 (direct)
GoaT chr no.:	42 (direct)
GoaT haploid no.:	21 (direct)
GoaT ploidy:	2 (ancestor)
ToLID prefix:	mRatNor

tolid	specimen_id	gal	sex	organism_part	biosample	biospecimen
mRatNor1	SAN0001274	SANGER INSTITUTE	MALE	KIDNEY	SAMEA7524437	SAMEA7524397
mRatNor1	SAN0001274	SANGER INSTITUTE	MALE	KIDNEY	SAMEA7524437	SAMEA7524397
mRatNor1	SAN0001274	SANGER INSTITUTE	MALE	KIDNEY	SAMEA7524437	SAMEA7524397
mRatNor1	SAN0001274	SANGER INSTITUTE	MALE	KIDNEY	SAMEA7524437	SAMEA7524397
mRatNor1	SAN0001274	SANGER INSTITUTE	MALE	KIDNEY	SAMEA7524437	SAMEA7524397

Spectra estimates

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

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source	specimen	k-mer	k-cov	haploid size	repeat (%)	heterozygosity (%)	model fit (%)	model error (%)	histogram
pacbio	mRatNor6	31	41.59	2,592,488,680	21.05	0.60	90.60	0.12	histogram.txt
htag-202110	mRatNor6	31	66.41	3,006,832,363	30.66	0.24	98.31	0.34	histogram.txt
pacbio	mRatNor10	31	13.37	2,004,767,334	27.85	1.81	98.57	0.19	histogram.txt
pacbio	mRatNor9	31	17.3	2,370,598,866	22.24	1.14	95.25	0.13	histogram.txt
10x	mRatNor1	31	15.33	3,310,516,797	37.06	0.64	98.62	0.73	histogram.txt
hic-arima	mRatNor1	31	36.05	2,544,891,374	20.73	0.40	99.15	0.44	histogram.txt
pacbio	mRatNor7	31	37.89	34,135,372	89.92	3.03	85.59	5.51	histogram.txt
pacbio	mRatNor8	31	15.79	2,649,566,472	21.90	0.39	96.97	0.13	histogram.txt
htag-202203	mRatNor5	31	37.75	2,776,540,286	23.68	0.28	98.61	0.33	histogram.txt

pipeline	specimen	date	run id	movie	well	tag	yield	N50	sample accession
PacBio - CLR	mRatNor1	2019-06-18	69793	m64016_190618_103014	A01	-	137,363,443,853	39,053	SAMN16261960
PacBio - CLR	mRatNor1	2019-06-22	69905	m64016_190622_041831	B01	-	127,339,986,206	35,554	SAMN16261960
PacBio - HiFi	mRatNor6	2021-09-09	86456	m64230e_210909_152906	A01	1012	5,767,304,402	13,858
PacBio - HiFi	mRatNor7	2021-09-09	86456	m64230e_210909_152906	A01	1012	5,767,304,402	13,858
PacBio - HiFi	mRatNor6	2021-09-10	86456	m64230e_210910_213825	B01	1012	9,242,807,942	13,846
PacBio - HiFi	mRatNor7	2021-09-10	86456	m64230e_210910_213825	B01	1012	9,242,807,942	13,846
PacBio - HiFi	mRatNor6	2021-11-15	87992	m64222e_211115_183322	A01	-	26,240,446,829	9,922
PacBio - HiFi	mRatNor8	2021-11-15	87992	m64222e_211115_183322	A01	-	28,844,118,522	9,930
PacBio - HiFi	mRatNor6	2021-11-17	87992	m64222e_211117_052750	B01	-	25,750,770,754	10,045
PacBio - HiFi	mRatNor9	2021-11-17	87992	m64222e_211117_052750	B01	-	28,541,162,119	10,050
PacBio - HiFi	mRatNor6	2021-11-18	87992	m64222e_211118_162435	C01	-	26,788,998,990	11,133
PacBio - HiFi	mRatNor10	2021-11-18	87992	m64222e_211118_162435	C01	-	29,617,082,180	11,150
PacBio - HiFi	mRatNor6	2021-11-25	88189	m64222e_211125_025537	B01	-	26,868,942,755	9,780
PacBio - HiFi	mRatNor8	2021-11-25	88189	m64222e_211125_025537	B01	-	29,222,798,276	9,798
PacBio - HiFi	mRatNor6	2021-11-26	88326	m64174e_211126_173648	A01	-	25,809,924,955	9,905
PacBio - HiFi	mRatNor6	2021-11-26	88189	m64222e_211126_135237	C01	-	27,092,532,219	9,819
PacBio - HiFi	mRatNor9	2021-11-26	88326	m64174e_211126_173648	A01	-	28,543,645,061	9,912
PacBio - HiFi	mRatNor8	2021-11-26	88189	m64222e_211126_135237	C01	-	29,451,774,240	9,839
PacBio - HiFi	mRatNor6	2021-11-28	88326	m64174e_211128_025442	B01	-	25,904,746,229	9,884
PacBio - HiFi	mRatNor6	2021-11-28	88189	m64222e_211128_005046	D01	-	24,957,328,321	10,967

id	taxon	similarity	seq	country	latitude	longitude
GBMND52211-21	Rattus norvegicus	0.9979	COI-5P	Cyprus	[object Object]	[object Object]
GBMND52210-21	Rattus norvegicus	0.9979	COI-5P	[object Object]	[object Object]	[object Object]
GBMA19095-19	Rattus norvegicus	0.9982	COI-5P	Cambodia	[object Object]	[object Object]
GBMA22959-19	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA16825-17	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA16823-17	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA16815-17	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA16812-17	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA16811-17	Rattus norvegicus	0.9984	COI-5P	China	[object Object]	[object Object]
GBMA3283-12	Rattus norvegicus	0.9984	COI-5P	[object Object]	[object Object]	[object Object]

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

pipeline	specimen	date	run id	read pairs	yield	sample accession	run status	barcode
Haplotagging	mRatNor6	2022-03-29	41305_1#3	550,800,716	81,793,906,326		qc complete	Rattus norvegicus (1.00)
Haplotagging	mRatNor6	2022-03-28	41302_2#3	644,565,430	95,717,966,355		qc complete
Haplotagging	mRatNor6	2022-03-29	41306#3	1,134,632,002	168,492,852,297		qc complete	Rattus norvegicus (1.00)
Haplotagging	mRatNor6	2022-03-29	41305_2#3	577,200,628	85,714,293,258		qc complete	Rattus norvegicus (0.99)
Haplotagging	mRatNor6	2022-03-28	41302_1#3	600,155,254	89,123,055,219		qc complete
Chromium genome	mRatNor1	2019-06-12	29703_1#3	134,746,922	20,346,785,222	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_1#4	159,392,818	24,068,315,518	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_2#3	139,778,240	21,106,514,240	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_1#1	190,271,588	28,731,009,788	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_2#1	196,855,598	29,725,195,298	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_1#2	134,555,188	20,317,833,388	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_2#2	139,178,772	21,015,994,572	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Chromium genome	mRatNor1	2019-06-12	29703_2#4	164,548,402	24,846,808,702	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Hi-C - Arima v2	mRatNor1	2020-01-13	32564_8#1	869,465,662	131,289,314,962	SAMN16261960	qc complete	Rattus norvegicus (1.00)
Hi-C - Arima v2	mRatNor1	2020-01-13	32564_7#1	865,528,386	130,694,786,286	SAMN16261960	qc complete	Rattus norvegicus (1.00)
-	mRatNor5	-	43968#11	66,911,868	9,936,412,398		-	Rattus norvegicus (1.00)
-	mRatNor5	-	43969#27	50,953,620	7,566,612,570		-	Rattus norvegicus (1.00)
-	mRatNor5	-	43968#32	57,139,938	8,485,280,793		-	Rattus norvegicus (1.00)
-	mRatNor5	-	43968#30	65,320,044	9,700,026,534		-	Rattus norvegicus (1.00)
-	mRatNor5	-	43968#15	73,545,952	10,921,573,872		-	Rattus norvegicus (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
0.991166	[7041 seqs] AC_000069.1 Rattus norvegicus strain BN; Sprague-Dawley chromosome 1, alternate assembly Rn_Celera, whole genome shotgun sequence [...]
0.910314	NC_001506.1 Murine osteosarcoma virus, complete genome
0.907417	NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome
0.902135	NC_001499.1 Abelson murine leukemia virus, complete genome
0.901381	[2 seqs] NC_008513.1 Buchnera aphidicola BCc, complete genome [...]
0.900394	NC_021929.1 Malvastrum leaf curl Philippines betasatellite, complete sequence

Showing 1 to 6 of 6 rows

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
mRatNor6
mRatNor1

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

Assemblies

In-progress assembly QC.

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

Organelles

In-progress organelle results from MitoHiFi or Oatk.

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

Rattus norvegicus

Info

Specimens

Spectra estimates

Sequence data

PacBio run data

ONT run data

Illumina run data

Cobionts

Assemblies

Organelles

Rattus norvegicus

Mash screen

MarkerScan: species composition

MarkerScan: cobiont assembly

Readviz classification

Contigviz classification