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

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

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.
¹Paired l32q20 = paired reads had the RRL restriction tag trimmed to 32 bp and were filtered for a minimum per base quality of 20;
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;
³Neither end = none of the reads of a read pair mapped to the reference;
⁴One end = only one read of a read pair was mapped;
⁵Diff chr = both reads of a read pair mapped, but to different chromosomes;
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;
⁷Too long = both reads of a read pair mapped at a larger distance from each other than expected;
⁸Relative orientation = reads of a read pair mapped in another orientation relative to each other than expected based on the reference chicken genome.

ISSN: 1471-2164