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Table 1 Melon genome sequence improvement metrics

From: Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

 

Whole genome

 

v3.5

 

Post-PAGIT1

Scaffolds

1,599

 

1,599

Contigs

29,865

 

20,406

Length (bp)

375,485,313

 

375,516,019

Length, no Ns (bp) 2

336,097,046

 

337,325,315

Stretches of Ns 3 (#N > 1)

28,306

 

20,295

Stretches of Ns 3 (#N = 20) 4

9,133

 

2,581

Number of Ns

39,388,267 (10.5%)

 

38,190,704 (10.2%)

Length of scaffolds (bp)

361,983,232

 

362,182,953

Length of scaffolds, no Ns (bp) 2

322,595,151

 

323,992,316

Length of contigs (bp)

13,502,081

 

13,333,066

Length of contigs, no Ns (bp) 2

13,501,895

 

13,332,999

Illumina unmapped reads (%) 5

18.3

 

13.9

Corrected sequence errors 6

   

       1 bp substitution errors

  

53.771

       1-3 bp insertion errors

  

46.659

       1-3 bp deletion errors

  

121.178

 

4235-4331 fragment

 

v3.5

Post-PAGIT 1

Final

Length (bp)

1,118,599

1,120,734

1,066,373

Stretches of Ns (#N > 1)

120

84

27

Number of Ns

202,018 (18%)

192,656 (17.1%)

57,617 (5.4%)

Average N-stretch size (bp)

1,656

2,007

1,859

  1. 1Immediately after prinseq processing step performed following iCORN/redundancy removal steps.
  2. 2Only A, T, C, and G, not N, are counted.
  3. 3Contiguous strings of Ns.
  4. 4Most 20 bp-long gaps produced by the assembler while building the reference assembly mark adjacent contigs that overlap but for the presence of short, low quality/wrong sequences at their ends. These gaps are good targets for IMAGE, the software responsible for closing gaps in the PAGIT toolkit, which removes end-sequence from contigs while attempting to extend them with re-sequencing data and to overlap adjacent contigs.
  5. 5Unmapped reads after aligning the set of DHL92 high-quality Illumina PE (see Methods section).
  6. 6Based on the output reports of the iCORN software.
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BMC Genomics

ISSN: 1471-2164

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