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Table 1 Assembly and annotation of the cheetah genome

From: Genomic legacy of the African cheetah, Acinonyx jubatus

Number Feature   Size Source
  Genome sequence and assembly 7 cheetahs   
1 A. jubatus raineyii (Tanzania) 3 cheetahs 75 × reference Table S2
2 A. jubatus jubatus (Namibia) 4 cheetahs 5 × resequencing Table S2
3 SOAP deNovo assembly    Tables S1, S4
4 Assisted assembly with domestic cat Fca-6.2 Fca-6.2 framework anchors:   Table S5
   a. Radiation Hybrid map 3000 markers  
   b. Linkage map 60,000 SNVs  
5 Estimated genome size (assembly and 17-mer)   2.375–2.395 Gb Table S3
6 N50 contigs   28.2 kbp Table S4
7 N50 scaffolds   3.1 Mb Table S4
8 Average GC content   0.475 Figure S3
  Annotation
9 Coding genes 20,343 genes 601.2 Mb Table S10
10 Non-coding RNA 200,045 loci   17 Mb Table S11
   a. 43,878 microRNA 4.41 Mb Table S11
   b. 1,605 small nuclear RNA 186 kbp Table S11
   c. 154,031 transport RNA 12.7 Mb Table S11
   d. 531 ribosomal RNA 85 kbp Table S11
11 Single nucleotide variants (SNVs)   1,820,419 loci Tables S15–S20
12 Repetitive elements Interspersed repeats 746 Mb Tables S6, S7
  39.48 % of cheetah genome Tandem repeats 51.2 Mb Table S8
   Complex tandem repeats 2.04 Mb Table S9
   3,126 loci   
   Microsatellites 23.47 Mb Table S8
   487,898 loci   
13 Genomic rearrangements of cheetah vs domestic cat   93 Mb Figures S5, S6
     Tables S13, S14
14 Nuclear mitochondrial segments   105.6 kbp Table S12
15 Positively selected genes   946 genes Datasheet S5
16 GARfield Genome Browser http://garfield.dobzhanskycenter.org