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Table 2 454 Read Pre-processing

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

Category Paired Linear
Titanium 454 Plates 0.5 0.5
Raw Reads (unbroken) 654,164 568,399
Raw Sequence (Mbp) 239.5 205.3
Average Raw Read Length (bp) 366.0 361.0
1Raw Coverage 79.8 68.4
Stage I - Split Pairs   
Reads 910,019 568,399
Sequence (Mbp) 201 205.3
Average Read Length (bp) 220.9 361.0
Stage I Coverage 67.0 68.4
Stage II - Trim/Contamination Removal   
Reads 496,756 338,957
Sequence (Mbp) 121.7 125.4
Average Read Length (bp) 244.9 367.9
Stage II Coverage 40.6 41.8
Stage III - Mate Pair Detection   
Reads 371,430 338,957
Sequence (Mbp) 67.3 125.4
Average Read Length (bp) 181.3 367.9
Stage III Coverage 22.4 41.8
  1. 1Based on 3 Mbp sub-genome size.