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  • Anomalous assembly.
Organism name:
Felis catus (domestic cat)
Infraspecific name:
Breed: Abyssinian
Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine
Assembly level:
Genome representation:
Assembly anomaly:
Excluded from RefSeq:
  • contaminated
  • superseded by newer assembly for species
GenBank assembly accession:
GCA_000181335.4 (replaced)
RefSeq assembly accession:
GCF_000181335.3 (suppressed) see latest RefSeq assembly for this species
RefSeq assembly and GenBank assembly identical:
no (hide details)
  • Only in RefSeq: chromosome MT
  • Data displayed for GenBank version
WGS Project:
Assembly method:
Celera Assembler v. 8.3rc2; Canu v. 1.6; Pilon v. 1.23
Expected final version:
Reference guided assembly:
felCat 9.0

IDs: 1448961 [UID] 5671478 [GenBank] 5705068 [RefSeq]

See Genome Information for Felis catus

There are 5 assemblies for this organism

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History (Show revision history)


Assembly Release Notes for domestic cat assembly, version Felis catus 9.0:
 A female Abyssinian cat named Cinnamon kept by Dr. Kristina Narfstrom at the University of Missouri was used as the DNA source for all sequencing reads. High molecular ... weight DNA was extracted from an early passage fibroblast cell line that was expanded in culture. From this source we at the McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO, and the Texas A&M Agrilife Genomics core facility have generated approx. 72x sequence coverage on the RSII and Sequel platforms. All sequence reads were assembled using the WTDBG software to create our initial contig assembly, followed by scaffolding of all possible contigs with a de novo Bionano map created from the same DNA source. 
 To create a chromosomal version of the 9.0 assembly we used Chromonomer (http://catchenlab.life.illinois.edu/chromonomer/) and marker sequences associated with a high-density SNP array-based genetic linkage map (Li et al., 2016) to order and orient all possible scaffolds. In addition, the assembled cat genome was aligned against the previous cat release (Felis catus 8.0).The assembled cat genome (version 9.0) was broken into 1kb segments and then aligned against the Felis catus 8.0 using BLAT (Kent 2002) to identify uniquely aligning segments of the cat genome to aid in identifying breakpoints. BLAT alignments with the Felis catus 8.0 genome were then used to refine the order and orientation information as well as to insert additional scaffolds into the conditional scaffold framework provided by the initial alignments and marker assignments. Finished BAC clones were also integrated into the assembly after this step. Finally, satellite sequences were identified in the genome, and centromeres were placed along each chromosome using the localization data inferred from radiation hybrid (Davis et al. 2009) and genetic linkage maps (Li et al. 2016) in combination with the localization of cat satellite sequences. 
 There are 2.46Gb bases (including Ns in gaps) on ordered/oriented chromosomes, 15Mb on the chr*_random, and 46Mb on chromosome Un. The scaffold N50 length is 147Mb (count=7) and the contig N50 length is 42 Mb (count=18). The chromosomal agp contains the ordered/oriented bases for each chromosome (named after the respective linkage group). This draft assembly is referred to as Felis_catus_9.0. 
 Funding sources: Nestle Purina, St Louis, MO gift to WCW; Winn Feline Foundation grants MT14-009 and W15-008 to WJM, WCW and LAL, and Morris Animal Foundation grant D16FE-011 to WJM.
 DNA source - Dr. Kristina Narfstrom, University of Missouri, Columbia, MO. 
 Sequencing - Wesley Warren, McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO; Bill Murphy, Texas A&M University, College Station, TX; Nestle Purina, St Louis, MO.
 BAC sequencing - McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO 
 Sequence assembly and data integration for creation of chromosomal AGP files - McDonnell Genome Institute at Washington University School of Medicine, St Louis, MO
 Cat RH and linkage maps - Bill Murphy and Gang Li, Texas A&M University, College Station, TX; Lesie Lyons, University of Missouri, Columbia, MO.

In version 9.1 the submitter was able to assemble the X chromosome into a single contiguous sequence. Since only the X chromosome was updated the genome version was not changed and will remain version 4. The contigs (AANG04000277, AANG04000391, AANG04000471, AANG04000480, AANG04000501, AANG04000511, AANG04000558, AANG04000778, AANG04000879, AANG04001034, AANG04001118, AANG04001236, AANG04001271, AANG04001293, AANG04001347, AANG04001348, AANG04001507, AANG04001513, AANG04001690, AANG04001722, AANG04001755, AANG04001840, AANG04001886, AANG04002019, AANG04002054, AANG04002097, AANG04002111, AANG04002134, AANG04002159, AANG04002273, AANG04002273, AANG04002462, AANG04002514, AANG04002641, AANG04002829, AANG04002836, AANG04002924, AANG04002986, AANG04003038, AANG04003470, AANG04003539, AANG04003579, AANG04003829, AANG04003847, AANG04004011, AANG04004069, AANG04004234, AANG04004236, AANG04004266, AANG04004274, AANG04004335, AANG04004376, AANG04004407, AANG04004457) and Scaffolds (KZ451880, KZ451881) which make up the previous version of the X chromosome have been removed from the assembly. The new X chromosome sequence (AANG04004909) was added to the end of the existing assembly and the corresponding chromosome record (CM001396.4) has been updated  more

Global statistics

Total sequence length2,521,846,836
Total ungapped length2,476,436,195
Gaps between scaffolds19
Number of scaffolds4,524
Scaffold N5083,967,707
Scaffold L5011
Number of contigs4,908
Contig N5041,915,695
Contig L5019
Total number of chromosomes and plasmids19
Number of component sequences (WGS or clone)4,997

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCA_000181345.4)
Molecule nameGenBank sequenceRefSeq sequenceUnlocalized
sequences count
Chromosome A1CM001378.3=NC_018723.310
Chromosome A2CM001379.3=NC_018724.324
Chromosome A3CM001380.3=NC_018725.318
Chromosome B1CM001381.3=NC_018726.311
Chromosome B2CM001382.3=NC_018727.328
Chromosome B3CM001383.3=NC_018728.321
Chromosome B4CM001384.3=NC_018729.324
Chromosome C1CM001385.3=NC_018730.323
Chromosome C2CM001386.3=NC_018731.318
Chromosome D1CM001387.3=NC_018732.331
Chromosome D2CM001388.3=NC_018733.314
Chromosome D3CM001389.3=NC_018734.314
Chromosome D4CM001390.3=NC_018735.310
Chromosome E1CM001391.3=NC_018736.315
Chromosome E2CM001392.3=NC_018737.318
Chromosome E3CM001393.3=NC_018738.37
Chromosome F1CM001394.3=NC_018739.328
Chromosome F2CM001395.3=NC_018740.36
Chromosome XCM001396.3=NC_018741.326

Assembly statistics

MoleculeSequence RoleTotal
AllAssembled molecule2,521,846,8364,5242,476,436,19583,967,70738419
Chromosome A1AllAssembled moleculeUnlocalized scaffolds242,507,196242,100,913406,28312210240,505,598240,099,315406,283151,220,850151,220,85050,743880110
Chromosome A2AllAssembled moleculeUnlocalized scaffolds172,636,169171,471,7471,164,42226224168,995,506167,831,0841,164,422109,391,014109,391,01456,84422220110
Chromosome A3AllAssembled moleculeUnlocalized scaffolds144,016,939143,202,405814,53420218141,627,440140,812,906814,53490,345,42990,345,42948,00512120110
Chromosome B1AllAssembled moleculeUnlocalized scaffolds208,708,019208,212,889495,13013211206,707,819206,212,689495,130167,918,410167,918,41044,013220110
Chromosome B2AllAssembled moleculeUnlocalized scaffolds156,711,270155,302,6381,408,63230228153,956,250152,547,6181,408,632124,136,783124,136,78362,521770110
Chromosome B3AllAssembled moleculeUnlocalized scaffolds150,747,685149,751,809995,87623221148,693,375147,697,499995,876119,088,311119,088,31151,495550110
Chromosome B4AllAssembled moleculeUnlocalized scaffolds145,661,306144,528,6951,132,61126224143,623,080142,490,4691,132,61198,720,21198,720,21150,151990110
Chromosome C1AllAssembled moleculeUnlocalized scaffolds223,892,009222,790,1421,101,86725223221,633,364220,531,4971,101,867112,883,106112,883,10652,0631731730110
Chromosome C2AllAssembled moleculeUnlocalized scaffolds161,947,688161,193,150754,53820218159,902,789159,148,251754,53883,967,70783,967,70760,381330110
Chromosome D1AllAssembled moleculeUnlocalized scaffolds119,003,985117,648,0281,355,95733231116,373,062115,017,1051,355,95783,463,34583,463,34549,08618180110
Chromosome D2AllAssembled moleculeUnlocalized scaffolds90,898,16590,186,660711,5051621488,722,68188,011,176711,50568,373,80668,373,80662,338660110
Chromosome D3AllAssembled moleculeUnlocalized scaffolds97,382,98096,884,206498,7741621494,692,54194,193,767498,77464,103,48364,103,48355,38618180110
Chromosome D4AllAssembled moleculeUnlocalized scaffolds97,051,20596,521,652529,5531221094,775,72994,246,176529,55362,995,65562,995,65564,91414140110
Chromosome E1AllAssembled moleculeUnlocalized scaffolds64,049,29363,494,689554,6041721562,048,79361,494,189554,60436,631,72436,631,72440,996550110
Chromosome E2AllAssembled moleculeUnlocalized scaffolds65,149,65964,340,295809,3642021862,973,53562,164,171809,36438,410,87838,410,87854,56213130110
Chromosome E3AllAssembled moleculeUnlocalized scaffolds44,908,72844,648,284260,44492741,689,57141,429,127260,44424,914,98024,914,98038,010880110
Chromosome F1AllAssembled moleculeUnlocalized scaffolds72,553,99571,664,243889,7522912870,388,46269,498,710889,75269,664,24369,664,24346,394550110
Chromosome F2AllAssembled moleculeUnlocalized scaffolds86,000,57385,752,456248,11771684,000,27383,752,156248,11783,752,45683,752,45644,543330110
Chromosome XAllAssembled moleculeUnlocalized scaffolds131,911,830130,557,0091,354,82128226129,105,045127,750,2241,354,82178,035,65378,035,65361,49452520110
unplacedAssembled molecule46,108,1424,14246,021,28212,61810