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Table 1 Plasmodium yoelii nigeriensis N67 genome assembly statistics using Hierarchical Genome Assembly Process (HGAP)

From: Genome sequence, transcriptome, and annotation of rodent malaria parasite Plasmodium yoelii nigeriensis N67

Assembly Statistics N67
Number of Contigs: 121
Number of chromosomes in the reference (17X): 16
Number of assembly bases: 21,277,183
Number of reference bases: 23,083,521
Number of LCBs: 11
Number of Blocks: 214
Breakpoint Distance: 204
DCJ Distance: 19
SCJ Distance: 408
Number of Gaps in Reference: 35,690
Number of Gaps in Assembly: 31,011
Number of missing chromosomes: 2
Number of extra contigs: 20
Number of Shared Boundaries: 0
Number of Inter-LCB Boundaries: 9
Contig N50: 300,848
Contig N90: 5956
Min contig length: 5956
Max contig length: 979,279
NG50 290,851
NA50 193,872
G + C content (%) 21.72
  1. Descriptions of the blocks of alignments and statistics identified by Mauve: LCB is defined as a set of local alignments that occur in the same order and orientation (free from internal rearrangement) in a pair of genomes. SCJ (Single-Cut-or-Join) and DCJ (double-cut-and-join) distances are rearrangement metrics that measure the minimum number of cut or join operations needed to transform one genome into another, whereas breakpoint distance is the number of non-conserved adjacencies.
  2. GC (%) is the total number of G and C nucleotides in the assembly, divided by the total length of the assembly.
  3. N50 is the length for which the collection of all contigs of that length or longer covers at least half (90% for N90) of the assembly.
  4. NG50 is the length for which the collection of all contigs of that length or longer covers at least half the reference genome.
  5. NA50 is similar to N50 (corresponding metric without “A”), based on aligned blocks instead of contigs