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Source database (GenBank or RefSeq) File type

mLynCan4.pri.v2

Organism name:

Lynx canadensis (Canada lynx)

Isolate:

LIC74

Sex:

male

BioSample:

SAMN09948483

BioProject:

PRJNA489107

Submitter:

Vertebrate Genomes Project

Date:

2020/07/14

Assembly type:

haploid (principal pseudohaplotype of diploid)

Assembly level:

Chromosome

Genome representation:

full

RefSeq category:

representative genome

GenBank assembly accession:

GCA_007474595.2 (latest)

RefSeq assembly accession:

GCF_007474595.2 (latest)

RefSeq assembly and GenBank assembly identical:

no (hide details)

Only in GenBank: chromosome MT

Data displayed for RefSeq version

WGS Project:

VHLE02

Assembly method:

FALCON v. 5.1.1; FALCON-Unzip v. 1.0.2; purge_haplotigs v. bitbucket 7.10.2018; scaff10x v. 2.1; Bionano Solve 2 enzyme v. 3.2.1; Salsa2 v. 2.2; Arrow v. 5.1.0.26412; longranger align v. 2.2.2; freebayes v. 1.2.0; gEVAL manual curation v. 2020-04-03; VGP standard assembly pipeline v. 1.5

Expected final version:

Genome coverage:

72.0x

Sequencing technology:

PacBio Sequel I; 10X genome; Bionano Genomics; Arima Genomics Hi-C

Linked assembly:

GCA_007474575.2 (alternate pseudohaplotype of diploid)

IDs: 7357471 [UID] 20354128 [GenBank] 21843908 [RefSeq]

See Genome Information for Lynx canadensis

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

GenBank Assembly Accession		RefSeq Assembly Accession	Assembly Name	Assembly Level	Status
GCA_007474595.2	≠	GCF_007474595.2	mLynCan4.pri.v2	Chromosome	Latest GenBank, Latest RefSeq
GCA_007474595.1	≠	GCF_007474595.1	mLynCan4_v1.p	Chromosome	Replaced GenBank, Replaced RefSeq

Comment

This assembly represents the principal haplotype of the diploid genome Lynx canadensis and includes the chromosomes. The alternate haplotype sequences are in WGS project VHLF00000000

Global statistics

Total sequence length	2,407,810,255
Total ungapped length	2,405,030,913
Gaps between scaffolds	0
Number of scaffolds	54
Scaffold N50	147,275,701
Scaffold L50	7
Number of contigs	894
Contig N50	7,503,561
Contig L50	94
Total number of chromosomes and plasmids	20
Number of component sequences (WGS or clone)	54

Molecule name	GenBank sequence		RefSeq sequence	Unlocalized sequences count
Chromosome A1	CM017329.2	=	NC_044303.2	0
Chromosome A2	CM017330.2	=	NC_044304.2	0
Chromosome A3	CM017331.1	=	NC_044305.1	0
Chromosome B1	CM017332.2	=	NC_044306.2	0
Chromosome B2	CM017333.1	=	NC_044307.1	0
Chromosome B3	CM017334.2	=	NC_044308.2	0
Chromosome B4	CM017335.1	=	NC_044309.1	0
Chromosome C1	CM017336.1	=	NC_044310.1	0
Chromosome C2	CM017337.2	=	NC_044311.2	0
Chromosome D1	CM017338.2	=	NC_044312.2	0
Chromosome D2	CM017339.2	=	NC_044313.2	0
Chromosome D3	CM017340.2	=	NC_044314.2	0
Chromosome D4	CM017341.2	=	NC_044315.2	0
Chromosome E1	CM017342.2	=	NC_044316.2	0
Chromosome E2	CM017343.1	=	NC_044317.1	0
Chromosome E3	CM017344.1	=	NC_044318.1	0
Chromosome F1	CM017345.2	=	NC_044319.2	0
Chromosome F2	CM017346.2	=	NC_044320.2	0
Chromosome X	CM017347.2	=	NC_044321.2	0
Chromosome Y	CM023961.1	=	NC_050200.1	4
unplaced	n/a	n/a	n/a	30

Molecule	Sequence Role	Total Length	Scaffold Count	Ungapped Length	Scaffold N50	Spanned Gaps	Unspanned Gaps
All	Assembled molecule	2,407,810,255	54	2,405,030,913	147,275,701	840	0
Chromosome A1	Assembled molecule	240,012,660	1	240,006,153	240,012,660	63	0
Chromosome A2	Assembled molecule	168,988,343	1	168,653,215	168,988,343	55	0
Chromosome A3	Assembled molecule	139,831,168	1	139,731,333	139,831,168	39	0
Chromosome B1	Assembled molecule	205,934,466	1	205,857,484	205,934,466	49	0
Chromosome B2	Assembled molecule	152,753,185	1	152,369,612	152,753,185	43	0
Chromosome B3	Assembled molecule	147,275,701	1	146,788,833	147,275,701	65	0
Chromosome B4	Assembled molecule	141,311,636	1	141,232,116	141,311,636	51	0
Chromosome C1	Assembled molecule	220,954,660	1	220,832,710	220,954,660	62	0
Chromosome C2	Assembled molecule	158,927,374	1	158,698,684	158,927,374	44	0
Chromosome D1	Assembled molecule	115,715,915	1	115,595,493	115,715,915	31	0
Chromosome D2	Assembled molecule	87,252,839	1	87,249,100	87,252,839	29	0
Chromosome D3	Assembled molecule	93,546,183	1	93,453,008	93,546,183	44	0
Chromosome D4	Assembled molecule	94,005,490	1	94,001,745	94,005,490	31	0
Chromosome E1	Assembled molecule	60,670,153	1	60,536,709	60,670,153	26	0
Chromosome E2	Assembled molecule	61,563,313	1	61,559,640	61,563,313	28	0
Chromosome E3	Assembled molecule	41,050,830	1	40,858,489	41,050,830	30	0
Chromosome F1	Assembled molecule	69,073,222	1	69,071,059	69,073,222	22	0
Chromosome F2	Assembled molecule	83,270,606	1	83,266,180	83,270,606	38	0
Chromosome X	Assembled molecule	122,536,723	1	122,397,361	122,536,723	78	0
Chromosome Y	AllAssembled moleculeUnlocalized scaffolds	2,048,7281,924,741123,987	514	1,785,8921,661,905123,987	1,924,7411,924,74131,503	10100	000
unplaced	Assembled molecule	1,087,060	30	1,086,097	39,736	2	0

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mLynCan4.pri.v2

See Genome Information for Lynx canadensis

Pathogen Detection Resources

There are 2 assemblies for this organism

History (Show revision history)

Comment

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