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Table 2 Summary of GS FLX Long Paired End assemblies

From: Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

  PE only PE+SG PE+SG+BE S0022P24
Large contigsa (> 500 bp) 310 289 286 14
Average contig size (bp) 2686 3058 3149 8885
N50 contig sizeb (bp) 4160 4728 5635 32866
Contigs assembed into scaffoldsc 203 186 175 9h
Total scaffolds 9 3 4 2
Large scaffoldsd (> 10 Kb) 6 3 4 2
Average large scaffold size (bp) 96257 299378 226679 112155
Largest scaffold size (bp) 227111 501016 538994 137857
N50 scaffold sizee (bp) 197327 361606 538994 137857
Total gapsf 194 183 171 8
Maximum gap size (bp) 1,881 2,100 2,131 unknown
Minimum gap size (bp) 4 4 8 unknown
Pair distance averageg (bp) 2680 2776 2782 N/A
Pair distance deviation (bp) 670 694 696 N/A
Total bases covering region 958507 1002840 1000926 231017
Depth of coverage ~26× ~56× ~56× ~10.5×
  1. Results for GS FLX Long Range Paired End (PE) assembly alone and when combined with the GS FLX shotgun (SG) data and BAC-end (BE) sequences. aContigs are defined as more than one read joined by overlapping sequence. Large contigs are greater than 500 bp. bThe N50 contig size is defined as the largest contig size at which half of the total size of the contigs is represented by contigs larger than the N50 value. cA scaffold is defined as two or more contigs associated by paired ends. dLarge scaffolds are those consisting of more than 10,000 bp among all contigs therein. eThe N50 scaffold size is defined as the largest scaffold size at which half of the total size of the scaffolds is represented by scaffolds larger than the N50 value. fGaps represent unsequenced regions between two contigs known to be adjacent due to associated paired ends. gAverage pair distance is the average distance between two sections of BAC DNA separated by linker sequence. hAssembly based on large contigs (> 500 bp) consisting of ≥3 reads each.