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Table 3 Basic assembly statistics for various read mixes

From: Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

454 Read Mix1 Scaffolds
total
Scaffolds
anchored
Scaffold Length (bp) Anchored Length (%) Match Score2 Relocation Score2 Inversion Score2 Coverage Score2 Gap Length (%N) Subgenome length (bp)
35L-20PP 16 5 2,925,652 96.5% 0.64 1.00 1.00 0.93 0.05% 3,032,287
20PP-20NM 23 5 2,948,378 95.6% 0.59 1.00 1.00 0.93 0.23% 3,085,172
10PP-10NM 20 9 2,919,380 96.1% 0.57 0.99 0.89 0.93 0.56% 3,037,466
20L-10PP 15 8 2,848,345 97.0% 0.56 1.00 1.00 0.92 0.88% 2,937,025
20L-15PP 14 7 2,894,304 96.7% 0.56 1.00 1.00 0.93 0.51% 2,993,053
20L-20PP 17 7 2,921,393 96.7% 0.56 1.00 1.00 0.93 0.30% 3,021,076
15PP-15NM 19 6 2,932,591 95.8% 0.55 1.00 1.00 0.93 0.39% 3,060,041
10L-20PP 13 7 2,917,670 96.6% 0.54 1.00 1.00 0.93 0.23% 3,021,711
15L-20PP 12 6 2,910,841 96.7% 0.54 1.00 1.00 0.93 0.29% 3,009,135
5L-20PP 15 6 2,874,297 94.5% 0.54 1.00 1.00 0.93 0.87% 3,040,453
10L-15PP 18 8 2,884,836 96.5% 0.53 1.00 1.00 0.92 0.74% 2,988,073
15L-15PP 15 8 2,892,073 96.7% 0.53 1.00 1.00 0.93 0.61% 2,989,876
5L-15PP 15 7 2,845,042 96.6% 0.53 1.00 1.00 0.92 1.48% 2,945,611
0L-20PP 13 6 2,877,053 94.9% 0.52 1.00 1.00 0.93 0.90% 3,031,950
10L-10PP 19 10 2,835,308 96.0% 0.52 1.00 1.00 0.91 1.02% 2,953,066
15L-10PP 16 8 2,835,593 96.8% 0.52 1.00 1.00 0.91 0.96% 2,928,679
20L-5PP 30 8 2,650,829 87.7% 0.52 0.99 0.94 0.72 2.84% 3,022,574
5L-10PP 25 10 2,734,631 96.2% 0.52 1.00 1.00 0.90 1.54% 2,843,359
0L-10PP 23 9 2,738,500 96.5% 0.51 0.93 0.78 0.90 1.68% 2,838,999
0L-15PP 17 7 2,836,521 94.5% 0.51 1.00 1.00 0.92 1.70% 3,001,136
10L-5PP 42 12 2,491,349 80.5% 0.51 0.89 0.38 0.66 5.20% 3,096,682
15L-5PP 34 9 2,588,122 84.3% 0.51 0.98 0.79 0.66 3.96% 3,068,882
5L-5PP 57 17 2,248,580 75.2% 0.51 0.91 0.62 0.66 7.06% 2,989,391
0L-5PP 57 17 2,214,995 74.7% 0.50 0.90 0.21 0.61 8.84% 2,967,162
35L-0PP 174 35 2,911,931 48.4% 0.50 0.99 0.28 0.51 0.00% 6,013,556
20L-0PP 70 26 1,812,591 59.4% 0.44 1.00 0.06 0.28 0.00% 3,048,991
10L-0PP 41 20 1,033,618 64.5% 0.40 1.00 0.55 0.17 0.00% 1,601,933
15L-0PP 57 23 1,485,809 59.2% 0.40 1.00 0.13 0.14 0.00% 2,510,749
5L-0PP 29 12 631,622 57.4% 0.27 1.00 0.12 0.07 0.00% 1,100,803
  1. 1Number = fold sequencing depth; L = linear (shotgun) reads; PP = true pair reads; NM = Unmated (shotgun) reads.