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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
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BMC Genomics

ISSN: 1471-2164

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