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Table 1 Sequencing and mapping results for the four chicken breeds analyzed for structural variation

From: Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries

Sequencing Mapping
Breed Raw reads Paired l32q201 Concordant2% Neither end3% One end4% Diff chr5% Too short6 Too long7 Relative orientation8
Brown egg layer 31.61 23.59 76.14 23.22 0.52 0.02 470 22547 549
White egg layer 29.70 21.84 73.30 25.81 0.64 0.14 1019 22058 1872
Broiler 1 34.82 24.83 78.26 21.14 0.48 0.01 2108 21209 335
Broiler 2 32.28 20.64 76.60 22.64 0.54 0.07 7388 22058 1030
  1. Paired-end sequencing of RRLs resulted in the indicated number of raw reads per breed. Sequencing read counts are in millions. Mapping percentages are relative to Paired l32q20.
  2. 1Paired l32q20 = paired reads had the RRL restriction tag trimmed to 32 bp and were filtered for a minimum per base quality of 20;
  3. 2Concordant = both reads of a read pair mapped to the expected orientation relative to each other and in the expected distance according to the RRL size range;
  4. 3Neither end = none of the reads of a read pair mapped to the reference;
  5. 4One end = only one read of a read pair was mapped;
  6. 5Diff chr = both reads of a read pair mapped, but to different chromosomes;
  7. 6Too short = both reads of a read pair mapped to the expected orientation relative to each other but at a closer distance than expected based on the RRL size range;
  8. 7Too long = both reads of a read pair mapped at a larger distance from each other than expected;
  9. 8Relative orientation = reads of a read pair mapped in another orientation relative to each other than expected based on the reference chicken genome.