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Table 2 Summary of the C. melo physical map FPC assemblies.

From: Generation of a BAC-based physical map of the melon genome

Tests for
initial cutoff valuea
Contigs Singletons Physical
length (Mb)
Q clonesb        
Test 1e-35 1420 1133 398 40/233        
Test 1e-45 1706 1772 421 40/158        
Test 1e-55 1909 2562 432 29/84        
Test 1e-65 2075 3399 438 12/44        
Assembly
Steps c
Contigs Singletons Physical
length (Mb)
Q clones b Longest
contig (Mb)
Number of contigs
(number of contigs with > 5% Q-clones) d
       ≥ 100 99-50 49-25 24-10 9-3 = 2
Initial 1e-45 1706 1772 1.17 421 40/158 0(0) 6(5) 63(36) 393(89) 968(28) 276(0)
DQer
(1e-48 to 1e-90)
1777 1923 1.10 428 66/0 0 1 49 412 1027 288
Merge 1e-40 1750 1551 1.10 432 66/0 0 2 51 431 1017 249
Merge 1e-35 1714 1290 1.10 430 66/0 0 2 56 442 998 216
Merge 1e-30 1650 1071 1.4 426 66/0 1 3 62 449 953 182
Merge 1e-25 1577 836 1.5 421 65/0 2 3 69 462 884 157
Merge 1e-20 1491 635 2.8 415 64/0 3 5 79 456 816 132
Merge 1e-15 1355 441 3.2 407 62/0 3 9 102 428 706 107
  1. aAn initial test to determine the optimal cutoff value was performed with several cutoff values in the 1e-35/1e-65 range
  2. bNumber of contigs containing ≤/> than 5% of Q-clones
  3. cA cutoff value of 1e-45 was used for the initial contig assembly. Consecutive DQer (for contigs containing > 5% Q-clones), end-merge and singleton-merge steps were performed to minimize the number of singletons, contigs and Q-clones
  4. dDistribution according to the number of clones belonging to each contig