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Table 1 Quantity and quality of paired-end sequencing reads

From: Mobile element scanning (ME-Scan) by targeted high-throughput sequencing

  Replication experiment Pooling experiment
Quality classification # read pairs % of total # read pairs % of total
Total read pairs 3,047,279 100 2,389,900 100
Both reads of high quality (not a, b or c, below) 2,998,412 98.4 2,315,412 96.9
   (a) Either read is > 85% any one base 1,370 0.0450 1,628 0.0681
   (b) Either read has > 2 'N' base calls 4,345 0.143 3,073 0.13
   (c) Adapter sequence detected in either read 43,192 1.42 69,827 2.9
Both reads high quality, index valid 2,963,735 97.3 2,287,571 95.7
Junction read has Alu sequence; both reads high quality; index valid 2,874,329 94.3 2,201,101 92.1
Supports an Alu insertion in the final results* 2,458,549 80.7 1,753,750 73.4
  1. *Supports one of the 5,053 insertion loci reported in Additional File 1.